Starting phenix.real_space_refine
on Wed Sep 17 16:43:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6j_50226/09_2025/9f6j_50226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6j_50226/09_2025/9f6j_50226.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6j_50226/09_2025/9f6j_50226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6j_50226/09_2025/9f6j_50226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6j_50226/09_2025/9f6j_50226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6j_50226/09_2025/9f6j_50226.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.096
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      32      5.49       5
     S      53      5.16       5
     C    6123      2.51       5
     N    1662      2.21       5
     O    1877      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 9751
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1118, 9091
          Classifications: {'peptide': 1118}
          Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1059}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "T"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 367
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4827  SG  CYS A 651      39.716  19.391  53.715  1.00 58.40           S
  ATOM   4843  SG  CYS A 654      37.813  17.520  48.017  1.00 56.47           S
  ATOM   4909  SG  CYS A 663      43.920  16.788  49.787  1.00 48.76           S
  ATOM   5633  SG  CYS A 747      42.860  21.938  48.845  1.00 46.18           S

  Time building chain proxies: 2.37, per 1000 atoms: 0.24
  Number of scatterers: 9751
  At special positions: 0
  Unit cell: (105.12, 108.04, 110.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      53     16.00
     P      32     15.00
     O    1877      8.00
     N    1662      7.00
     C    6123      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: 0.92
  Conformation dependent library (CDL) restraints added in 351.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1301 "
        pdb="FE3  SF4 A1301 " - pdb=" SG  CYS A 663 "
        pdb="FE2  SF4 A1301 " - pdb=" SG  CYS A 654 "
        pdb="FE1  SF4 A1301 " - pdb=" SG  CYS A 651 "
        pdb="FE4  SF4 A1301 " - pdb=" SG  CYS A 747 "
      Number of angles added : 12


  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 12 sheets defined
      49.6% alpha, 16.0% beta
      13 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 48
    Processing helix  chain 'A' and resid 112 through 124
    Processing helix  chain 'A' and resid 143 through 147
    Processing helix  chain 'A' and resid 159 through 171
    Processing helix  chain 'A' and resid 171 through 181
      removed outlier: 4.030A  pdb=" N   LYS A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LYS A 176 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 236
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 3.675A  pdb=" N   GLU A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 379
      removed outlier: 3.538A  pdb=" N   PHE A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   HIS A 379 " --> pdb=" O   ARG A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 407 through 415
      removed outlier: 3.681A  pdb=" N   SER A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 422
    Processing helix  chain 'A' and resid 423 through 433
    Processing helix  chain 'A' and resid 440 through 442
      No H-bonds generated for 'chain 'A' and resid 440 through 442'
    Processing helix  chain 'A' and resid 443 through 451
    Processing helix  chain 'A' and resid 452 through 473
      removed outlier: 3.806A  pdb=" N   VAL A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   SER A 461 " --> pdb=" O   THR A 457 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ASP A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ALA A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA A 465 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   THR A 466 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 483
      removed outlier: 4.144A  pdb=" N   PHE A 477 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   PHE A 479 " --> pdb=" O   HIS A 475 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 496 through 512
      removed outlier: 3.984A  pdb=" N   VAL A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 573 through 584
      removed outlier: 3.891A  pdb=" N   ALA A 581 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 593
      removed outlier: 3.820A  pdb=" N   VAL A 593 " --> pdb=" O   VAL A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 613
      removed outlier: 3.537A  pdb=" N   VAL A 599 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS A 600 " --> pdb=" O   PHE A 596 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 639
    Processing helix  chain 'A' and resid 647 through 652
      removed outlier: 3.772A  pdb=" N   CYS A 651 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 691
      removed outlier: 3.557A  pdb=" N   ARG A 685 " --> pdb=" O   SER A 681 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU A 691 " --> pdb=" O   GLN A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 710
      No H-bonds generated for 'chain 'A' and resid 708 through 710'
    Processing helix  chain 'A' and resid 711 through 731
      removed outlier: 3.843A  pdb=" N   LYS A 729 " --> pdb=" O   ASP A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 786
    Processing helix  chain 'A' and resid 787 through 819
      removed outlier: 4.338A  pdb=" N   TYR A 816 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   VAL A 819 " --> pdb=" O   PHE A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 854
      removed outlier: 3.979A  pdb=" N   CYS A 836 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLY A 839 " --> pdb=" O   VAL A 835 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG A 847 " --> pdb=" O   ILE A 843 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ILE A 850 " --> pdb=" O   ALA A 846 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 853 " --> pdb=" O   LEU A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 906
      removed outlier: 3.814A  pdb=" N   LEU A 897 " --> pdb=" O   PRO A 893 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE A 899 " --> pdb=" O   ALA A 895 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   MET A 900 " --> pdb=" O   MET A 896 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR A 906 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 975
    Processing helix  chain 'A' and resid 979 through 994
      removed outlier: 3.619A  pdb=" N   GLU A 991 " --> pdb=" O   SER A 987 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU A 994 " --> pdb=" O   PHE A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1020
      removed outlier: 4.184A  pdb=" N   LYS A1008 " --> pdb=" O   GLY A1004 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   VAL A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA A1010 " --> pdb=" O   VAL A1006 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TYR A1012 " --> pdb=" O   LYS A1008 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TRP A1013 " --> pdb=" O   VAL A1009 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   VAL A1016 " --> pdb=" O   TYR A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1034
      removed outlier: 3.926A  pdb=" N   GLU A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1047
    Processing helix  chain 'A' and resid 1051 through 1065
      removed outlier: 3.552A  pdb=" N   PHE A1063 " --> pdb=" O   ARG A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1070
      removed outlier: 4.730A  pdb=" N   VAL A1069 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1088 through 1091
    Processing helix  chain 'A' and resid 1097 through 1101
    Processing helix  chain 'A' and resid 1102 through 1114
    Processing helix  chain 'A' and resid 1123 through 1128
    Processing helix  chain 'A' and resid 1129 through 1145
      removed outlier: 3.730A  pdb=" N   TYR A1133 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   SER A1139 " --> pdb=" O   GLU A1135 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLN A1142 " --> pdb=" O   GLY A1138 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS A1143 " --> pdb=" O   SER A1139 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A1144 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1151
    Processing helix  chain 'A' and resid 1164 through 1175
      removed outlier: 3.636A  pdb=" N   ASN A1175 " --> pdb=" O   LEU A1171 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52
      removed outlier: 6.839A  pdb=" N   GLU A  51 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 8.322A  pdb=" N   ALA A  97 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE A  87 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   LEU A  63 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 136
      removed outlier: 3.720A  pdb=" N   ASP A 220 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 337
      removed outlier: 4.344A  pdb=" N   THR A 308 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   GLU A 337 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   MET A 294 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ALA A 277 " --> pdb=" O   MET A 294 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ILE A 296 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA A 275 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   TYR A 298 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ALA A 273 " --> pdb=" O   TYR A 298 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   ILE A 300 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   VAL A 271 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU A 272 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 361 " --> pdb=" O   MET A 405 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391
    Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 536
      removed outlier: 6.765A  pdb=" N   GLU A 674 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   THR A 745 " --> pdb=" O   VAL A 646 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 553
      removed outlier: 3.547A  pdb=" N   ALA A 939 " --> pdb=" O   PHE A 959 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561
    Processing sheet with id=AA8, first strand: chain 'A' and resid 855 through 859
      removed outlier: 3.592A  pdb=" N   ARG A 855 " --> pdb=" O   VAL A 867 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   TRP A 865 " --> pdb=" O   LEU A 857 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU A 859 " --> pdb=" O   GLY A 863 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLY A 863 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 695
    Processing sheet with id=AB1, first strand: chain 'A' and resid 875 through 879
    Processing sheet with id=AB2, first strand: chain 'A' and resid 907 through 913
      removed outlier: 5.848A  pdb=" N   ASP A 908 " --> pdb=" O   GLU A 926 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   GLU A 926 " --> pdb=" O   ASP A 908 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080

    429 hydrogen bonds defined for protein.
    1224 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      31 hydrogen bonds
      62 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.43: 4293
        1.43 -     1.64: 5662
        1.64 -     1.85: 78
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 10045
  Sorted by residual:
  bond pdb=" C3'  DA P  29 "
       pdb=" C2'  DA P  29 "
    ideal  model  delta    sigma   weight residual
    1.525  1.555 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" C4'  DA P  29 "
       pdb=" O4'  DA P  29 "
    ideal  model  delta    sigma   weight residual
    1.450  1.421  0.029 2.00e-02 2.50e+03 2.03e+00
  bond pdb=" C3'  DG P  28 "
       pdb=" C2'  DG P  28 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.05e-01
  bond pdb=" C2'  DA T  21 "
       pdb=" C1'  DA T  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.507  0.018 2.00e-02 2.50e+03 7.75e-01
  bond pdb=" O4'  DA P  29 "
       pdb=" C1'  DA P  29 "
    ideal  model  delta    sigma   weight residual
    1.414  1.397  0.017 2.00e-02 2.50e+03 7.26e-01
  ... (remaining 10040 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 13000
        1.32 -     2.65: 598
        2.65 -     3.97: 106
        3.97 -     5.30: 8
        5.30 -     6.62: 2
  Bond angle restraints: 13714
  Sorted by residual:
  angle pdb=" N   GLY A 330 "
        pdb=" CA  GLY A 330 "
        pdb=" C   GLY A 330 "
      ideal   model   delta    sigma   weight residual
     112.34  118.96   -6.62 2.04e+00 2.40e-01 1.05e+01
  angle pdb=" O3'  DA P  21 "
        pdb=" C3'  DA P  21 "
        pdb=" C2'  DA P  21 "
      ideal   model   delta    sigma   weight residual
     111.50  116.05   -4.55 1.50e+00 4.44e-01 9.20e+00
  angle pdb=" C2'  DA P  29 "
        pdb=" C1'  DA P  29 "
        pdb=" N9   DA P  29 "
      ideal   model   delta    sigma   weight residual
     113.50  117.86   -4.36 1.50e+00 4.44e-01 8.47e+00
  angle pdb=" N   ILE A 312 "
        pdb=" CA  ILE A 312 "
        pdb=" C   ILE A 312 "
      ideal   model   delta    sigma   weight residual
     112.12  109.74    2.38 8.40e-01 1.42e+00 8.03e+00
  angle pdb=" C4'  DA P  29 "
        pdb=" O4'  DA P  29 "
        pdb=" C1'  DA P  29 "
      ideal   model   delta    sigma   weight residual
     109.70  105.58    4.12 1.50e+00 4.44e-01 7.53e+00
  ... (remaining 13709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5358
       17.79 -    35.57: 472
       35.57 -    53.36: 127
       53.36 -    71.15: 44
       71.15 -    88.93: 18
  Dihedral angle restraints: 6019
    sinusoidal: 2720
      harmonic: 3299
  Sorted by residual:
  dihedral pdb=" CA  GLU A 438 "
           pdb=" C   GLU A 438 "
           pdb=" N   LEU A 439 "
           pdb=" CA  LEU A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.87   28.13     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  GLU A 337 "
           pdb=" C   GLU A 337 "
           pdb=" N   PRO A 338 "
           pdb=" CA  PRO A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.57  -26.43     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  PRO A1025 "
           pdb=" C   PRO A1025 "
           pdb=" N   ASP A1026 "
           pdb=" CA  ASP A1026 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.14  -23.86     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 6016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1025
       0.037 -    0.075: 326
       0.075 -    0.112: 99
       0.112 -    0.150: 26
       0.150 -    0.187: 4
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" C4'  DA P  29 "
            pdb=" C5'  DA P  29 "
            pdb=" O4'  DA P  29 "
            pdb=" C3'  DA P  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.34   -0.19 2.00e-01 2.50e+01 8.75e-01
  chirality pdb=" C3'  DG P  20 "
            pdb=" C4'  DG P  20 "
            pdb=" O3'  DG P  20 "
            pdb=" C2'  DG P  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.49   -0.17 2.00e-01 2.50e+01 7.31e-01
  chirality pdb=" CA  PHE A 905 "
            pdb=" N   PHE A 905 "
            pdb=" C   PHE A 905 "
            pdb=" CB  PHE A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.99e-01
  ... (remaining 1477 not shown)

  Planarity restraints: 1659
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 892 "   -0.016 2.00e-02 2.50e+03   2.60e-02 1.35e+01
        pdb=" CG  TYR A 892 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 892 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 892 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 892 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 892 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 892 "    0.025 2.00e-02 2.50e+03
        pdb=" OH  TYR A 892 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 671 "   -0.033 2.00e-02 2.50e+03   1.87e-02 8.77e+00
        pdb=" CG  TRP A 671 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 671 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 671 "    0.016 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 671 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 671 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 671 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 671 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 671 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 671 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 310 "   -0.223 9.50e-02 1.11e+02   1.01e-01 7.78e+00
        pdb=" NE  ARG A 310 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 310 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 310 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 310 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1656 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1935
        2.78 -     3.31: 9257
        3.31 -     3.84: 14978
        3.84 -     4.37: 17391
        4.37 -     4.90: 29728
  Nonbonded interactions: 73289
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 396 "
            pdb=" NH1 ARG A 494 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" ND2 ASN A 177 "
            pdb=" O   ASP A 216 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OG  SER A 643 "
            pdb=" OE2 GLU A 750 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OH  TYR A 100 "
            pdb=" OD2 ASP A 235 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OD1 ASP A 725 "
            pdb=" NH2 ARG A 728 "
     model   vdw
     2.339 3.120
  ... (remaining 73284 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.070
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
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   0.047  10049  Z= 0.136
  Angle     :  0.903  47.045  13726  Z= 0.395
  Chirality :  0.042   0.187   1480
  Planarity :  0.009   0.101   1659
  Dihedral  : 16.082  88.933   3883
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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: -1.09 (0.23), residues: 1114
  helix: -0.85 (0.21), residues: 453
  sheet: -0.15 (0.32), residues: 202
  loop : -0.63 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.003   ARG A 310 
 TYR   0.050   0.005   TYR A 892 
 PHE   0.028   0.004   PHE A 119 
 TRP   0.033   0.006   TRP A 671 
 HIS   0.011   0.002   HIS A 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10045)
  covalent geometry    : angle       0.64143 (13714)
  hydrogen bonds       : bond        0.14756 (  460)
  hydrogen bonds       : angle       7.19942 ( 1286)
  metal coordination   : bond        0.03407 (    4)
  metal coordination   : angle      21.50317 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TYR cc_start: 0.8885 (p90) cc_final: 0.8471 (p90)
REVERT: A  157 PHE cc_start: 0.8835 (m-80) cc_final: 0.8392 (m-10)
REVERT: A  397 TYR cc_start: 0.7417 (m-80) cc_final: 0.5931 (m-10)
REVERT: A  416 TYR cc_start: 0.7901 (m-80) cc_final: 0.7687 (m-10)
REVERT: A  601 ASP cc_start: 0.7940 (m-30) cc_final: 0.7714 (t0)
REVERT: A  688 HIS cc_start: 0.8493 (t-170) cc_final: 0.8241 (m170)
REVERT: A  791 VAL cc_start: 0.8192 (t) cc_final: 0.7712 (p)
REVERT: A  818 TYR cc_start: 0.8572 (t80) cc_final: 0.7131 (t80)
REVERT: A  857 LEU cc_start: 0.9259 (mt) cc_final: 0.8912 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1421
  time to fit residues: 35.4284
Evaluate side-chains
  85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0570
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.2504

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

Flipped N/Q/H residues before XYZ refinement:
A 229 HIS
A 394 GLN
** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 852 GLN
A 960 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.129664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.096204 restraints weight = 19924.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096529 restraints weight = 13829.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.096912 restraints weight = 10928.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.097531 restraints weight = 9864.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.097597 restraints weight = 8961.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10049  Z= 0.158
  Angle     :  0.694  27.260  13726  Z= 0.343
  Chirality :  0.043   0.152   1480
  Planarity :  0.005   0.044   1659
  Dihedral  : 15.614  88.418   1573
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  7.98 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.26 (0.25), residues: 1114
  helix:  0.56 (0.23), residues: 459
  sheet:  0.05 (0.34), residues: 207
  loop :  0.03 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 975 
 TYR   0.012   0.001   TYR A 754 
 PHE   0.027   0.002   PHE A 119 
 TRP   0.019   0.001   TRP A 671 
 HIS   0.013   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10045)
  covalent geometry    : angle       0.62086 (13714)
  hydrogen bonds       : bond        0.05170 (  460)
  hydrogen bonds       : angle       5.10722 ( 1286)
  metal coordination   : bond        0.00802 (    4)
  metal coordination   : angle      10.53279 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 TYR cc_start: 0.8851 (p90) cc_final: 0.8531 (p90)
REVERT: A  138 ASP cc_start: 0.8406 (t0) cc_final: 0.7287 (p0)
REVERT: A  157 PHE cc_start: 0.8869 (m-80) cc_final: 0.8415 (m-80)
REVERT: A  444 MET cc_start: 0.7562 (ptp) cc_final: 0.7318 (ptp)
REVERT: A  446 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7674 (ptp-170)
REVERT: A  688 HIS cc_start: 0.8614 (t-170) cc_final: 0.8309 (m170)
REVERT: A  779 LEU cc_start: 0.8083 (tt) cc_final: 0.7811 (tt)
REVERT: A 1165 ASP cc_start: 0.7458 (p0) cc_final: 0.7082 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1058
  time to fit residues: 18.2923
Evaluate side-chains
  95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  906 THR
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 422 HIS
A 580 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.129849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.097048 restraints weight = 19935.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.097220 restraints weight = 13742.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097685 restraints weight = 11335.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.098272 restraints weight = 9688.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.098396 restraints weight = 8812.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10049  Z= 0.124
  Angle     :  0.596  20.294  13726  Z= 0.302
  Chirality :  0.041   0.203   1480
  Planarity :  0.004   0.039   1659
  Dihedral  : 15.136  83.546   1573
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  9.49 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.65 (0.25), residues: 1114
  helix:  0.98 (0.24), residues: 458
  sheet:  0.22 (0.35), residues: 194
  loop :  0.13 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 976 
 TYR   0.012   0.001   TYR A1133 
 PHE   0.032   0.001   PHE A 971 
 TRP   0.015   0.001   TRP A 671 
 HIS   0.005   0.001   HIS A 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10045)
  covalent geometry    : angle       0.54842 (13714)
  hydrogen bonds       : bond        0.04321 (  460)
  hydrogen bonds       : angle       4.65987 ( 1286)
  metal coordination   : bond        0.00493 (    4)
  metal coordination   : angle       7.91420 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8520 (tmm-80)
REVERT: A   83 ASP cc_start: 0.7454 (m-30) cc_final: 0.6730 (p0)
REVERT: A  138 ASP cc_start: 0.8518 (t0) cc_final: 0.7419 (p0)
REVERT: A  221 MET cc_start: 0.8347 (ptp) cc_final: 0.8132 (ptp)
REVERT: A  447 MET cc_start: 0.8129 (mmt) cc_final: 0.7678 (mmp)
REVERT: A  688 HIS cc_start: 0.8611 (t-170) cc_final: 0.8361 (m170)
REVERT: A  783 VAL cc_start: 0.8086 (t) cc_final: 0.7850 (t)
REVERT: A 1165 ASP cc_start: 0.7413 (p0) cc_final: 0.7030 (m-30)
  outliers start: 25
  outliers final: 17
  residues processed: 114
  average time/residue: 0.1107
  time to fit residues: 17.5839
Evaluate side-chains
  96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  429 LYS
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  906 THR
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 75 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.127989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.095116 restraints weight = 20290.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.095222 restraints weight = 14278.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.095629 restraints weight = 11687.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.096190 restraints weight = 9964.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.096405 restraints weight = 9115.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10049  Z= 0.137
  Angle     :  0.602  21.792  13726  Z= 0.299
  Chirality :  0.041   0.150   1480
  Planarity :  0.004   0.040   1659
  Dihedral  : 15.175  82.984   1573
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.11 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.63 (0.25), residues: 1114
  helix:  1.00 (0.24), residues: 460
  sheet:  0.13 (0.35), residues: 202
  loop :  0.11 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 446 
 TYR   0.012   0.001   TYR A 244 
 PHE   0.029   0.002   PHE A 971 
 TRP   0.012   0.001   TRP A 671 
 HIS   0.004   0.001   HIS A1163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10045)
  covalent geometry    : angle       0.54861 (13714)
  hydrogen bonds       : bond        0.04495 (  460)
  hydrogen bonds       : angle       4.51629 ( 1286)
  metal coordination   : bond        0.00831 (    4)
  metal coordination   : angle       8.38261 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8557 (tmm-80)
REVERT: A   83 ASP cc_start: 0.7478 (m-30) cc_final: 0.6499 (p0)
REVERT: A  138 ASP cc_start: 0.8577 (t0) cc_final: 0.7524 (p0)
REVERT: A  221 MET cc_start: 0.8396 (ptp) cc_final: 0.8156 (ptp)
REVERT: A  244 TYR cc_start: 0.8709 (m-80) cc_final: 0.8002 (m-80)
REVERT: A  263 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8647 (mm)
REVERT: A  359 MET cc_start: 0.8663 (tpp) cc_final: 0.8073 (mpp)
REVERT: A  447 MET cc_start: 0.8138 (mmt) cc_final: 0.7840 (mmt)
REVERT: A  559 ARG cc_start: 0.7553 (tmm-80) cc_final: 0.6453 (ptt-90)
REVERT: A  688 HIS cc_start: 0.8659 (t-170) cc_final: 0.8362 (m170)
  outliers start: 30
  outliers final: 21
  residues processed: 107
  average time/residue: 0.1073
  time to fit residues: 16.1425
Evaluate side-chains
  103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  906 THR
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 109 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.126531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.093851 restraints weight = 20239.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.093934 restraints weight = 14604.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.094270 restraints weight = 12038.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.094862 restraints weight = 10209.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.095065 restraints weight = 9316.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  10049  Z= 0.156
  Angle     :  0.618  22.493  13726  Z= 0.303
  Chirality :  0.042   0.223   1480
  Planarity :  0.004   0.041   1659
  Dihedral  : 15.156  82.316   1573
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.73 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.56 (0.25), residues: 1114
  helix:  1.04 (0.24), residues: 458
  sheet:  0.08 (0.36), residues: 202
  loop : -0.02 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 446 
 TYR   0.010   0.001   TYR A 754 
 PHE   0.027   0.002   PHE A 971 
 TRP   0.011   0.001   TRP A 671 
 HIS   0.004   0.001   HIS A1168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10045)
  covalent geometry    : angle       0.55944 (13714)
  hydrogen bonds       : bond        0.04725 (  460)
  hydrogen bonds       : angle       4.57235 ( 1286)
  metal coordination   : bond        0.01003 (    4)
  metal coordination   : angle       8.86679 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8639 (tmm-80)
REVERT: A   83 ASP cc_start: 0.7545 (m-30) cc_final: 0.6428 (p0)
REVERT: A  138 ASP cc_start: 0.8717 (t0) cc_final: 0.7751 (p0)
REVERT: A  244 TYR cc_start: 0.8802 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  263 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8725 (mm)
REVERT: A  359 MET cc_start: 0.8683 (tpp) cc_final: 0.8176 (mpp)
REVERT: A  447 MET cc_start: 0.8159 (mmt) cc_final: 0.7926 (mmt)
REVERT: A  528 THR cc_start: 0.6500 (OUTLIER) cc_final: 0.6195 (p)
REVERT: A  559 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.6797 (ptt-90)
REVERT: A  688 HIS cc_start: 0.8665 (t-170) cc_final: 0.8396 (m170)
REVERT: A 1068 MET cc_start: 0.7084 (mmm) cc_final: 0.6799 (mmm)
  outliers start: 29
  outliers final: 22
  residues processed: 106
  average time/residue: 0.1037
  time to fit residues: 15.5613
Evaluate side-chains
  99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  429 LYS
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  906 THR
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.127998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.095719 restraints weight = 20247.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.095737 restraints weight = 13829.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.096205 restraints weight = 11837.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.096758 restraints weight = 9831.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.096927 restraints weight = 8978.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10049  Z= 0.124
  Angle     :  0.577  17.139  13726  Z= 0.289
  Chirality :  0.040   0.147   1480
  Planarity :  0.004   0.040   1659
  Dihedral  : 15.071  80.607   1573
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.23 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.64 (0.25), residues: 1114
  helix:  1.18 (0.24), residues: 461
  sheet:  0.18 (0.37), residues: 195
  loop : -0.11 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 446 
 TYR   0.010   0.001   TYR A1133 
 PHE   0.027   0.001   PHE A 971 
 TRP   0.012   0.001   TRP A 671 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10045)
  covalent geometry    : angle       0.53903 (13714)
  hydrogen bonds       : bond        0.04134 (  460)
  hydrogen bonds       : angle       4.31118 ( 1286)
  metal coordination   : bond        0.00572 (    4)
  metal coordination   : angle       6.94221 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8666 (tmm-80)
REVERT: A   83 ASP cc_start: 0.7529 (m-30) cc_final: 0.6429 (p0)
REVERT: A  138 ASP cc_start: 0.8675 (t0) cc_final: 0.7714 (p0)
REVERT: A  244 TYR cc_start: 0.8784 (m-80) cc_final: 0.7977 (m-80)
REVERT: A  263 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: A  359 MET cc_start: 0.8811 (tpp) cc_final: 0.8279 (mpp)
REVERT: A  528 THR cc_start: 0.6500 (OUTLIER) cc_final: 0.6197 (p)
REVERT: A  559 ARG cc_start: 0.7570 (tmm-80) cc_final: 0.6708 (ptt-90)
REVERT: A  562 MET cc_start: 0.8385 (mmm) cc_final: 0.8083 (mmm)
REVERT: A  688 HIS cc_start: 0.8634 (t-170) cc_final: 0.8374 (m170)
REVERT: A 1068 MET cc_start: 0.6861 (mmm) cc_final: 0.6510 (mmm)
  outliers start: 28
  outliers final: 21
  residues processed: 102
  average time/residue: 0.1081
  time to fit residues: 15.5793
Evaluate side-chains
  97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  906 THR
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1036 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.128931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.096684 restraints weight = 20161.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.096656 restraints weight = 14025.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.097233 restraints weight = 11490.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.097758 restraints weight = 9621.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097944 restraints weight = 8784.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10049  Z= 0.115
  Angle     :  0.558  16.224  13726  Z= 0.282
  Chirality :  0.040   0.134   1480
  Planarity :  0.004   0.041   1659
  Dihedral  : 15.011  79.127   1573
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.43 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.67 (0.25), residues: 1114
  helix:  1.30 (0.24), residues: 462
  sheet:  0.16 (0.37), residues: 195
  loop : -0.19 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 446 
 TYR   0.009   0.001   TYR A 754 
 PHE   0.026   0.001   PHE A 971 
 TRP   0.012   0.001   TRP A 671 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10045)
  covalent geometry    : angle       0.52296 (13714)
  hydrogen bonds       : bond        0.03908 (  460)
  hydrogen bonds       : angle       4.22599 ( 1286)
  metal coordination   : bond        0.00412 (    4)
  metal coordination   : angle       6.62059 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8668 (tmm-80)
REVERT: A   83 ASP cc_start: 0.7533 (m-30) cc_final: 0.6666 (p0)
REVERT: A  138 ASP cc_start: 0.8692 (t0) cc_final: 0.7688 (p0)
REVERT: A  244 TYR cc_start: 0.8737 (m-80) cc_final: 0.7952 (m-80)
REVERT: A  263 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8678 (mm)
REVERT: A  359 MET cc_start: 0.8799 (tpp) cc_final: 0.8285 (mpp)
REVERT: A  528 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6534 (p)
REVERT: A  559 ARG cc_start: 0.7563 (tmm-80) cc_final: 0.6694 (ptt-90)
REVERT: A  562 MET cc_start: 0.8503 (mmm) cc_final: 0.8295 (mmm)
REVERT: A  623 TYR cc_start: 0.8319 (m-10) cc_final: 0.8090 (m-10)
REVERT: A  688 HIS cc_start: 0.8580 (t-170) cc_final: 0.8347 (m170)
  outliers start: 28
  outliers final: 21
  residues processed: 95
  average time/residue: 0.1036
  time to fit residues: 13.8460
Evaluate side-chains
  95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  130 LYS
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  906 THR
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 109 optimal weight:    0.0020
   chunk 50 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 103 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.129997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098461 restraints weight = 19964.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098621 restraints weight = 12869.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.098994 restraints weight = 11338.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.099721 restraints weight = 9295.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.099871 restraints weight = 8302.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10049  Z= 0.109
  Angle     :  0.557  14.363  13726  Z= 0.279
  Chirality :  0.039   0.136   1480
  Planarity :  0.004   0.041   1659
  Dihedral  : 14.931  77.448   1573
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.94 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.79 (0.25), residues: 1114
  helix:  1.41 (0.25), residues: 460
  sheet:  0.22 (0.37), residues: 195
  loop : -0.14 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 446 
 TYR   0.016   0.001   TYR A 224 
 PHE   0.031   0.001   PHE A 971 
 TRP   0.011   0.001   TRP A 671 
 HIS   0.002   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10045)
  covalent geometry    : angle       0.52716 (13714)
  hydrogen bonds       : bond        0.03647 (  460)
  hydrogen bonds       : angle       4.14679 ( 1286)
  metal coordination   : bond        0.00302 (    4)
  metal coordination   : angle       6.14801 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8720 (tmm-80)
REVERT: A   83 ASP cc_start: 0.7507 (m-30) cc_final: 0.6659 (p0)
REVERT: A  103 TYR cc_start: 0.8500 (p90) cc_final: 0.8298 (p90)
REVERT: A  138 ASP cc_start: 0.8641 (t0) cc_final: 0.7590 (p0)
REVERT: A  244 TYR cc_start: 0.8688 (m-80) cc_final: 0.7929 (m-80)
REVERT: A  263 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8618 (mm)
REVERT: A  359 MET cc_start: 0.8786 (tpp) cc_final: 0.8233 (mpp)
REVERT: A  528 THR cc_start: 0.6800 (OUTLIER) cc_final: 0.6515 (p)
REVERT: A  559 ARG cc_start: 0.7503 (tmm-80) cc_final: 0.6680 (ptt-90)
REVERT: A  623 TYR cc_start: 0.8332 (m-10) cc_final: 0.8111 (m-10)
REVERT: A  688 HIS cc_start: 0.8553 (t-170) cc_final: 0.8337 (m170)
REVERT: A  993 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7352 (t80)
REVERT: A 1068 MET cc_start: 0.6432 (mmp) cc_final: 0.5965 (mmm)
  outliers start: 25
  outliers final: 17
  residues processed: 96
  average time/residue: 0.1030
  time to fit residues: 14.3208
Evaluate side-chains
  92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  445 CYS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1145 ILE
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0370
   chunk 5 optimal weight:    0.0370
   chunk 80 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.4136

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.130747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.097453 restraints weight = 19917.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.098845 restraints weight = 13580.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.100005 restraints weight = 9181.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.099926 restraints weight = 8325.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.100250 restraints weight = 7976.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10049  Z= 0.108
  Angle     :  0.551  13.766  13726  Z= 0.277
  Chirality :  0.039   0.179   1480
  Planarity :  0.004   0.041   1659
  Dihedral  : 14.854  75.929   1573
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.65 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.85 (0.25), residues: 1114
  helix:  1.49 (0.24), residues: 460
  sheet:  0.22 (0.36), residues: 203
  loop : -0.13 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 247 
 TYR   0.017   0.001   TYR A 224 
 PHE   0.019   0.001   PHE A 971 
 TRP   0.011   0.001   TRP A 671 
 HIS   0.002   0.000   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10045)
  covalent geometry    : angle       0.52161 (13714)
  hydrogen bonds       : bond        0.03555 (  460)
  hydrogen bonds       : angle       4.09616 ( 1286)
  metal coordination   : bond        0.00228 (    4)
  metal coordination   : angle       5.98258 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7501 (m-30) cc_final: 0.6649 (p0)
REVERT: A  103 TYR cc_start: 0.8489 (p90) cc_final: 0.8272 (p90)
REVERT: A  138 ASP cc_start: 0.8665 (t0) cc_final: 0.7652 (p0)
REVERT: A  244 TYR cc_start: 0.8670 (m-80) cc_final: 0.7943 (m-80)
REVERT: A  263 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8645 (mm)
REVERT: A  359 MET cc_start: 0.8802 (tpp) cc_final: 0.8264 (mpp)
REVERT: A  528 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6435 (p)
REVERT: A  559 ARG cc_start: 0.7460 (tmm-80) cc_final: 0.6666 (ptt-90)
REVERT: A  623 TYR cc_start: 0.8506 (m-10) cc_final: 0.8289 (m-10)
REVERT: A  688 HIS cc_start: 0.8666 (t-170) cc_final: 0.8380 (m170)
REVERT: A  993 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7317 (t80)
REVERT: A 1068 MET cc_start: 0.6516 (mmp) cc_final: 0.6222 (mmm)
  outliers start: 23
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1068
  time to fit residues: 15.2338
Evaluate side-chains
  92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue  995 LYS
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 105 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 96 optimal weight:    0.2980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.130154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.096679 restraints weight = 19955.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098047 restraints weight = 13387.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.098822 restraints weight = 9280.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099017 restraints weight = 8541.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.099249 restraints weight = 8048.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.4673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10049  Z= 0.113
  Angle     :  0.562  15.151  13726  Z= 0.281
  Chirality :  0.040   0.213   1480
  Planarity :  0.004   0.040   1659
  Dihedral  : 14.830  73.792   1573
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.85 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.87 (0.25), residues: 1114
  helix:  1.58 (0.24), residues: 456
  sheet:  0.22 (0.37), residues: 203
  loop : -0.19 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 446 
 TYR   0.012   0.001   TYR A 224 
 PHE   0.012   0.001   PHE A 971 
 TRP   0.015   0.001   TRP A1113 
 HIS   0.003   0.001   HIS A1108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10045)
  covalent geometry    : angle       0.53097 (13714)
  hydrogen bonds       : bond        0.03648 (  460)
  hydrogen bonds       : angle       4.07307 ( 1286)
  metal coordination   : bond        0.00355 (    4)
  metal coordination   : angle       6.24467 (   12)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ASP cc_start: 0.7499 (m-30) cc_final: 0.6654 (p0)
REVERT: A  103 TYR cc_start: 0.8501 (p90) cc_final: 0.8263 (p90)
REVERT: A  138 ASP cc_start: 0.8582 (t0) cc_final: 0.7704 (p0)
REVERT: A  244 TYR cc_start: 0.8712 (m-80) cc_final: 0.7961 (m-80)
REVERT: A  263 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8681 (mm)
REVERT: A  359 MET cc_start: 0.8809 (tpp) cc_final: 0.8291 (mpp)
REVERT: A  528 THR cc_start: 0.6414 (OUTLIER) cc_final: 0.6182 (p)
REVERT: A  559 ARG cc_start: 0.7476 (tmm-80) cc_final: 0.6698 (ptt-90)
REVERT: A  623 TYR cc_start: 0.8425 (m-10) cc_final: 0.8217 (m-10)
REVERT: A  688 HIS cc_start: 0.8677 (t-170) cc_final: 0.8382 (m170)
REVERT: A  993 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7114 (t80)
REVERT: A 1068 MET cc_start: 0.6552 (mmp) cc_final: 0.6121 (mmm)
  outliers start: 20
  outliers final: 14
  residues processed: 91
  average time/residue: 0.1023
  time to fit residues: 13.4779
Evaluate side-chains
  89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  736 ILE
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 93 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.129111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.097525 restraints weight = 19858.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098228 restraints weight = 13315.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.098587 restraints weight = 10367.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.099202 restraints weight = 9057.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.099293 restraints weight = 8244.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10049  Z= 0.123
  Angle     :  0.578  16.525  13726  Z= 0.286
  Chirality :  0.040   0.203   1480
  Planarity :  0.004   0.042   1659
  Dihedral  : 14.863  72.080   1573
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.44 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    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:  0.85 (0.25), residues: 1114
  helix:  1.57 (0.24), residues: 457
  sheet:  0.27 (0.37), residues: 195
  loop : -0.24 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 446 
 TYR   0.012   0.001   TYR A 224 
 PHE   0.031   0.001   PHE A 971 
 TRP   0.029   0.001   TRP A1113 
 HIS   0.003   0.001   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10045)
  covalent geometry    : angle       0.54312 (13714)
  hydrogen bonds       : bond        0.03848 (  460)
  hydrogen bonds       : angle       4.11530 ( 1286)
  metal coordination   : bond        0.00519 (    4)
  metal coordination   : angle       6.67503 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1444.94 seconds
wall clock time: 25 minutes 42.11 seconds (1542.11 seconds total)