Starting phenix.real_space_refine
on Wed Jul 30 14:45:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8b_36066/07_2025/8j8b_36066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8b_36066/07_2025/8j8b_36066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8b_36066/07_2025/8j8b_36066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8b_36066/07_2025/8j8b_36066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8b_36066/07_2025/8j8b_36066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8b_36066/07_2025/8j8b_36066.cif"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    7922      2.51       5
     N    2116      2.21       5
     O    2242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12330
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 759, 6165
          Classifications: {'peptide': 759}
          Link IDs: {'PTRANS': 30, 'TRANS': 728}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 13.99, per 1000 atoms: 1.13
  Number of scatterers: 12330
  At special positions: 0
  Unit cell: (108.73, 107.07, 112.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    2242      8.00
     N    2116      7.00
     C    7922      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.87
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2852

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 16 sheets defined
      50.2% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 428 through 431
    Processing helix  chain 'A' and resid 439 through 451
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 497 through 501
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 547 through 560
    Processing helix  chain 'A' and resid 560 through 566
      removed outlier: 3.942A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.603A  pdb=" N   LYS A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.587A  pdb=" N   HIS A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 642 through 653
      removed outlier: 3.818A  pdb=" N   LYS A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLU A 647 " --> pdb=" O   ASP A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 664
      removed outlier: 3.962A  pdb=" N   LYS A 661 " --> pdb=" O   SER A 657 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ARG A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLU A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 683
      removed outlier: 3.718A  pdb=" N   VAL A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 705
      removed outlier: 3.513A  pdb=" N   THR A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   LYS A 696 " --> pdb=" O   GLN A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 738 through 749
    Processing helix  chain 'A' and resid 754 through 765
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.686A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 847
      removed outlier: 3.619A  pdb=" N   GLU A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 877
    Processing helix  chain 'A' and resid 882 through 893
      removed outlier: 4.085A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A 892 " --> pdb=" O   TYR A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 952
    Processing helix  chain 'A' and resid 953 through 958
    Processing helix  chain 'A' and resid 982 through 991
      removed outlier: 4.196A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLU A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU A 989 " --> pdb=" O   ARG A 985 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS A 991 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1027 through 1070
      removed outlier: 3.729A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1081 through 1091
      removed outlier: 3.768A  pdb=" N   ILE A1088 " --> pdb=" O   GLU A1084 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A1089 " --> pdb=" O   ALA A1085 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU A1091 " --> pdb=" O   ARG A1087 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.526A  pdb=" N   LEU A1118 " --> pdb=" O   ASN A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1133
    Processing helix  chain 'A' and resid 1134 through 1160
      removed outlier: 3.575A  pdb=" N   ARG A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1187
    Processing helix  chain 'B' and resid 428 through 431
    Processing helix  chain 'B' and resid 439 through 451
    Processing helix  chain 'B' and resid 452 through 456
    Processing helix  chain 'B' and resid 497 through 501
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 522 through 527
    Processing helix  chain 'B' and resid 547 through 560
    Processing helix  chain 'B' and resid 560 through 566
      removed outlier: 3.942A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 602
      removed outlier: 3.603A  pdb=" N   LYS B 602 " --> pdb=" O   ALA B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.586A  pdb=" N   HIS B 631 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 642 through 653
      removed outlier: 3.818A  pdb=" N   LYS B 646 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLU B 647 " --> pdb=" O   ASP B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 664
      removed outlier: 3.961A  pdb=" N   LYS B 661 " --> pdb=" O   SER B 657 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ARG B 662 " --> pdb=" O   GLU B 658 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   GLU B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 683
      removed outlier: 3.719A  pdb=" N   VAL B 682 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 705
      removed outlier: 3.514A  pdb=" N   THR B 695 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   LYS B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 738 through 749
    Processing helix  chain 'B' and resid 754 through 765
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 3.687A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 847
      removed outlier: 3.618A  pdb=" N   GLU B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 877
    Processing helix  chain 'B' and resid 882 through 893
      removed outlier: 4.084A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS B 892 " --> pdb=" O   TYR B 888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 952
    Processing helix  chain 'B' and resid 953 through 958
    Processing helix  chain 'B' and resid 982 through 991
      removed outlier: 4.196A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   GLU B 988 " --> pdb=" O   ASN B 984 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU B 989 " --> pdb=" O   ARG B 985 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS B 991 " --> pdb=" O   VAL B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1070
      removed outlier: 3.729A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1081 through 1091
      removed outlier: 3.767A  pdb=" N   ILE B1088 " --> pdb=" O   GLU B1084 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU B1089 " --> pdb=" O   ALA B1085 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU B1091 " --> pdb=" O   ARG B1087 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1119
      removed outlier: 3.525A  pdb=" N   LEU B1118 " --> pdb=" O   ASN B1114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1129 through 1133
    Processing helix  chain 'B' and resid 1134 through 1160
      removed outlier: 3.575A  pdb=" N   ARG B1140 " --> pdb=" O   ALA B1136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419
      removed outlier: 6.182A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE A 685 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   THR A 638 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737
      removed outlier: 3.546A  pdb=" N   ILE A 782 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.544A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 850
    Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913
    Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 926
      removed outlier: 5.846A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A 962 " --> pdb=" O   LYS A 977 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1014 through 1016
    Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419
      removed outlier: 6.183A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   THR B 638 " --> pdb=" O   ILE B 685 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737
      removed outlier: 3.545A  pdb=" N   ILE B 782 " --> pdb=" O   SER B 802 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.544A  pdb=" N   VAL B 825 " --> pdb=" O   ALA B 832 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 850
    Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913
    Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 926
      removed outlier: 5.847A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU B 962 " --> pdb=" O   LYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016

    558 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.40

  Time building geometry restraints manager: 3.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3984
        1.34 -     1.46: 2820
        1.46 -     1.58: 5740
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 12622
  Sorted by residual:
  bond pdb=" CB  ASP A 414 "
       pdb=" CG  ASP A 414 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.00e+00
  bond pdb=" CB  ASP B 414 "
       pdb=" CG  ASP B 414 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.00e+00
  bond pdb=" CG  ARG A 734 "
       pdb=" CD  ARG A 734 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.74e-01
  bond pdb=" C   SER A1162 "
       pdb=" N   PRO A1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 2.34e-02 1.83e+03 5.71e-01
  bond pdb=" CG  ARG B 734 "
       pdb=" CD  ARG B 734 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.62e-01
  ... (remaining 12617 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 16542
        0.98 -     1.97: 387
        1.97 -     2.95: 83
        2.95 -     3.93: 31
        3.93 -     4.91: 11
  Bond angle restraints: 17054
  Sorted by residual:
  angle pdb=" C   GLY A 472 "
        pdb=" N   VAL A 473 "
        pdb=" CA  VAL A 473 "
      ideal   model   delta    sigma   weight residual
     121.97  126.27   -4.30 1.80e+00 3.09e-01 5.70e+00
  angle pdb=" C   GLY B 472 "
        pdb=" N   VAL B 473 "
        pdb=" CA  VAL B 473 "
      ideal   model   delta    sigma   weight residual
     121.97  126.22   -4.25 1.80e+00 3.09e-01 5.58e+00
  angle pdb=" CA  TYR B1122 "
        pdb=" CB  TYR B1122 "
        pdb=" CG  TYR B1122 "
      ideal   model   delta    sigma   weight residual
     113.90  109.92    3.98 1.80e+00 3.09e-01 4.89e+00
  angle pdb=" CA  TYR A1122 "
        pdb=" CB  TYR A1122 "
        pdb=" CG  TYR A1122 "
      ideal   model   delta    sigma   weight residual
     113.90  109.97    3.93 1.80e+00 3.09e-01 4.77e+00
  angle pdb=" N   PHE B1191 "
        pdb=" CA  PHE B1191 "
        pdb=" CB  PHE B1191 "
      ideal   model   delta    sigma   weight residual
     113.65  110.66    2.99 1.47e+00 4.63e-01 4.15e+00
  ... (remaining 17049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.89: 6827
       11.89 -    23.78: 534
       23.78 -    35.67: 175
       35.67 -    47.57: 34
       47.57 -    59.46: 8
  Dihedral angle restraints: 7578
    sinusoidal: 3128
      harmonic: 4450
  Sorted by residual:
  dihedral pdb=" CA  TYR A1122 "
           pdb=" C   TYR A1122 "
           pdb=" N   THR A1123 "
           pdb=" CA  THR A1123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  TYR B1122 "
           pdb=" C   TYR B1122 "
           pdb=" N   THR B1123 "
           pdb=" CA  THR B1123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  PRO B 938 "
           pdb=" C   PRO B 938 "
           pdb=" N   LEU B 939 "
           pdb=" CA  LEU B 939 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.63  -17.37     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 7575 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1294
       0.034 -    0.068: 414
       0.068 -    0.102: 92
       0.102 -    0.135: 46
       0.135 -    0.169: 2
  Chirality restraints: 1848
  Sorted by residual:
  chirality pdb=" CB  VAL B 473 "
            pdb=" CA  VAL B 473 "
            pdb=" CG1 VAL B 473 "
            pdb=" CG2 VAL B 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CB  VAL A 473 "
            pdb=" CA  VAL A 473 "
            pdb=" CG1 VAL A 473 "
            pdb=" CG2 VAL A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.10e-01
  chirality pdb=" CA  ILE B 685 "
            pdb=" N   ILE B 685 "
            pdb=" C   ILE B 685 "
            pdb=" CB  ILE B 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1845 not shown)

  Planarity restraints: 2176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 937 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A 938 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO B 938 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1122 "   -0.020 2.00e-02 2.50e+03   1.10e-02 2.41e+00
        pdb=" CG  TYR A1122 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1122 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1122 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1122 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1122 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1122 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A1122 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2173 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1329
        2.75 -     3.29: 12051
        3.29 -     3.82: 20379
        3.82 -     4.36: 25542
        4.36 -     4.90: 43217
  Nonbonded interactions: 102518
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 712 "
            pdb=" NH1 ARG A 719 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OD2 ASP B 712 "
            pdb=" NH1 ARG B 719 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG  SER B 919 "
            pdb=" OD1 ASN B1007 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER A 919 "
            pdb=" OD1 ASN A1007 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER B 787 "
            pdb=" OD2 ASP B 794 "
     model   vdw
     2.244 3.040
  ... (remaining 102513 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.780
  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:             0.020
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     37.800
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:19.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12622  Z= 0.096
  Angle     :  0.415   4.914  17054  Z= 0.227
  Chirality :  0.038   0.169   1848
  Planarity :  0.003   0.041   2176
  Dihedral  :  9.831  59.457   4726
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.22), residues: 1510
  helix:  1.30 (0.20), residues: 658
  sheet:  0.23 (0.40), residues: 198
  loop :  0.38 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 820 
 HIS   0.004   0.001   HIS B1078 
 PHE   0.007   0.001   PHE B 990 
 TYR   0.022   0.001   TYR A1122 
 ARG   0.010   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24014 (  558)
  hydrogen bonds       : angle       6.38442 ( 1572)
  covalent geometry    : bond        0.00211 (12622)
  covalent geometry    : angle       0.41463 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 MET cc_start: 0.8665 (ptp) cc_final: 0.8372 (ptp)
REVERT: B  701 ASP cc_start: 0.8147 (t70) cc_final: 0.7762 (t70)
REVERT: B  888 TYR cc_start: 0.8843 (t80) cc_final: 0.8640 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 106
  average time/residue: 1.5380
  time to fit residues: 176.1584
Evaluate side-chains
  74 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.5980
   chunk 113 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   chunk 76 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 136 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.086721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.062484 restraints weight = 22412.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 2.72
r_work: 0.2680 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2550 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12622  Z= 0.158
  Angle     :  0.510   6.608  17054  Z= 0.279
  Chirality :  0.042   0.144   1848
  Planarity :  0.004   0.042   2176
  Dihedral  :  4.030  20.235   1684
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.65 %
    Favored  : 94.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.22), residues: 1510
  helix:  1.18 (0.20), residues: 690
  sheet:  0.05 (0.40), residues: 180
  loop :  0.12 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 599 
 HIS   0.002   0.001   HIS A 650 
 PHE   0.010   0.001   PHE B 649 
 TYR   0.030   0.001   TYR B1122 
 ARG   0.009   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04933 (  558)
  hydrogen bonds       : angle       4.68946 ( 1572)
  covalent geometry    : bond        0.00360 (12622)
  covalent geometry    : angle       0.50957 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.9024 (ptt) cc_final: 0.8690 (ptp)
REVERT: A  659 LEU cc_start: 0.8562 (mt) cc_final: 0.8347 (mm)
REVERT: A  662 ARG cc_start: 0.8458 (mpt-90) cc_final: 0.8140 (mpp80)
REVERT: A  701 ASP cc_start: 0.8580 (t70) cc_final: 0.8313 (t70)
REVERT: A  915 GLN cc_start: 0.9132 (pt0) cc_final: 0.8920 (pt0)
REVERT: A 1048 MET cc_start: 0.8891 (mtm) cc_final: 0.8574 (mtp)
REVERT: B  662 ARG cc_start: 0.8196 (mpp80) cc_final: 0.7717 (mpp80)
REVERT: B  701 ASP cc_start: 0.8480 (t70) cc_final: 0.8196 (t70)
REVERT: B  915 GLN cc_start: 0.9155 (pt0) cc_final: 0.8927 (pt0)
REVERT: B 1041 GLU cc_start: 0.8614 (pt0) cc_final: 0.8355 (mm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 91
  average time/residue: 1.3884
  time to fit residues: 137.4862
Evaluate side-chains
  75 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue 1110 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 133 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
B1099 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.082464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.057900 restraints weight = 22894.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 2.73
r_work: 0.2580 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2448 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  12622  Z= 0.275
  Angle     :  0.606  13.568  17054  Z= 0.320
  Chirality :  0.046   0.141   1848
  Planarity :  0.006   0.084   2176
  Dihedral  :  4.708  25.551   1684
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  6.98 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.22), residues: 1510
  helix:  1.07 (0.20), residues: 686
  sheet: -0.64 (0.37), residues: 192
  loop : -0.13 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 856 
 HIS   0.005   0.001   HIS A1012 
 PHE   0.013   0.002   PHE A 990 
 TYR   0.029   0.002   TYR B1122 
 ARG   0.011   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  558)
  hydrogen bonds       : angle       4.59390 ( 1572)
  covalent geometry    : bond        0.00661 (12622)
  covalent geometry    : angle       0.60602 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  455 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8437 (t)
REVERT: A  635 MET cc_start: 0.9080 (ptt) cc_final: 0.8741 (ptp)
REVERT: A  915 GLN cc_start: 0.9171 (pt0) cc_final: 0.8954 (pt0)
REVERT: A 1087 ARG cc_start: 0.7895 (ptm-80) cc_final: 0.7602 (mtm-85)
REVERT: A 1143 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8248 (pp20)
REVERT: B  635 MET cc_start: 0.8995 (ptt) cc_final: 0.8789 (ptp)
REVERT: B  662 ARG cc_start: 0.8438 (mpp80) cc_final: 0.8044 (mpp80)
REVERT: B  701 ASP cc_start: 0.8509 (t70) cc_final: 0.8290 (t70)
  outliers start: 13
  outliers final: 5
  residues processed: 84
  average time/residue: 1.6691
  time to fit residues: 151.1411
Evaluate side-chains
  72 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  922 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0970
   chunk 99 optimal weight:    0.8980
   chunk 104 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.085038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.060760 restraints weight = 22473.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 2.71
r_work: 0.2647 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12622  Z= 0.134
  Angle     :  0.505  13.195  17054  Z= 0.265
  Chirality :  0.041   0.136   1848
  Planarity :  0.004   0.046   2176
  Dihedral  :  4.376  23.984   1684
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.03 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.22), residues: 1510
  helix:  1.20 (0.20), residues: 688
  sheet: -0.68 (0.37), residues: 190
  loop : -0.14 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 820 
 HIS   0.002   0.001   HIS A1099 
 PHE   0.010   0.001   PHE A 990 
 TYR   0.026   0.001   TYR A1122 
 ARG   0.010   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  558)
  hydrogen bonds       : angle       4.39179 ( 1572)
  covalent geometry    : bond        0.00308 (12622)
  covalent geometry    : angle       0.50517 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 ARG cc_start: 0.8558 (mpt-90) cc_final: 0.8235 (mpp80)
REVERT: A  915 GLN cc_start: 0.9151 (pt0) cc_final: 0.8945 (pt0)
REVERT: A  988 GLU cc_start: 0.8667 (pt0) cc_final: 0.8254 (pp20)
REVERT: A 1048 MET cc_start: 0.8926 (mtm) cc_final: 0.8600 (mtp)
REVERT: A 1087 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7575 (mtm-85)
REVERT: B  924 ASP cc_start: 0.8600 (m-30) cc_final: 0.8181 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 85
  average time/residue: 1.5341
  time to fit residues: 141.3354
Evaluate side-chains
  75 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 129 optimal weight:    0.0070
   chunk 52 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0870
   chunk 93 optimal weight:    2.9990
   chunk 128 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
B1099 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.085181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.060888 restraints weight = 22405.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 2.71
r_work: 0.2647 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12622  Z= 0.131
  Angle     :  0.497  11.398  17054  Z= 0.262
  Chirality :  0.041   0.171   1848
  Planarity :  0.004   0.051   2176
  Dihedral  :  4.299  24.106   1684
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.48 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.22), residues: 1510
  helix:  1.26 (0.20), residues: 688
  sheet: -0.71 (0.38), residues: 190
  loop : -0.12 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.028   0.001   TYR A1122 
 ARG   0.012   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  558)
  hydrogen bonds       : angle       4.29976 ( 1572)
  covalent geometry    : bond        0.00301 (12622)
  covalent geometry    : angle       0.49713 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 ARG cc_start: 0.8606 (mpt-90) cc_final: 0.8220 (mpp80)
REVERT: A  915 GLN cc_start: 0.9159 (pt0) cc_final: 0.8951 (pt0)
REVERT: A  924 ASP cc_start: 0.8592 (m-30) cc_final: 0.8184 (m-30)
REVERT: A  988 GLU cc_start: 0.8646 (pt0) cc_final: 0.8266 (pp20)
REVERT: A 1048 MET cc_start: 0.8914 (mtm) cc_final: 0.8599 (mtp)
REVERT: A 1087 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7569 (mtm-85)
REVERT: B  924 ASP cc_start: 0.8614 (m-30) cc_final: 0.8203 (m-30)
REVERT: B 1048 MET cc_start: 0.8920 (mtm) cc_final: 0.8591 (mtp)
  outliers start: 12
  outliers final: 6
  residues processed: 82
  average time/residue: 1.4550
  time to fit residues: 129.8604
Evaluate side-chains
  73 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue  922 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 143 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 98 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   chunk 111 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 510 GLN
B 510 GLN
B1099 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.085204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.060858 restraints weight = 22667.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 2.76
r_work: 0.2643 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2509 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12622  Z= 0.133
  Angle     :  0.495  11.434  17054  Z= 0.260
  Chirality :  0.041   0.179   1848
  Planarity :  0.004   0.051   2176
  Dihedral  :  4.281  24.141   1684
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.01 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.22), residues: 1510
  helix:  1.31 (0.21), residues: 688
  sheet: -0.71 (0.38), residues: 190
  loop : -0.11 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.031   0.001   TYR A1122 
 ARG   0.014   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  558)
  hydrogen bonds       : angle       4.21590 ( 1572)
  covalent geometry    : bond        0.00309 (12622)
  covalent geometry    : angle       0.49456 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  988 GLU cc_start: 0.8646 (pt0) cc_final: 0.8274 (pp20)
REVERT: A 1048 MET cc_start: 0.8887 (mtm) cc_final: 0.8568 (mtp)
REVERT: A 1087 ARG cc_start: 0.7915 (ptm-80) cc_final: 0.7564 (mtm-85)
REVERT: B  454 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8981 (mtmm)
REVERT: B  660 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7743 (ttp-170)
REVERT: B  662 ARG cc_start: 0.8457 (mpp80) cc_final: 0.7770 (mpp80)
REVERT: B  924 ASP cc_start: 0.8575 (m-30) cc_final: 0.8354 (m-30)
REVERT: B 1048 MET cc_start: 0.8879 (mtm) cc_final: 0.8565 (mtp)
  outliers start: 10
  outliers final: 7
  residues processed: 77
  average time/residue: 1.5375
  time to fit residues: 128.4707
Evaluate side-chains
  75 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue  922 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 138 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 131 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 129 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.084684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.060397 restraints weight = 22565.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 2.71
r_work: 0.2634 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2502 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12622  Z= 0.149
  Angle     :  0.500  11.024  17054  Z= 0.264
  Chirality :  0.042   0.193   1848
  Planarity :  0.004   0.053   2176
  Dihedral  :  4.311  24.452   1684
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.01 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.22), residues: 1510
  helix:  1.31 (0.21), residues: 688
  sheet: -0.73 (0.38), residues: 190
  loop : -0.14 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.030   0.001   TYR A1122 
 ARG   0.014   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  558)
  hydrogen bonds       : angle       4.21216 ( 1572)
  covalent geometry    : bond        0.00350 (12622)
  covalent geometry    : angle       0.49986 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 1.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8973 (mmmt)
REVERT: A  924 ASP cc_start: 0.8577 (m-30) cc_final: 0.8354 (m-30)
REVERT: A  988 GLU cc_start: 0.8639 (pt0) cc_final: 0.8289 (pp20)
REVERT: A 1048 MET cc_start: 0.8919 (mtm) cc_final: 0.8621 (mtp)
REVERT: A 1087 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7581 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8990 (mt0) cc_final: 0.8669 (mm110)
REVERT: B  454 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8994 (mtmm)
REVERT: B  660 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7755 (ttp-170)
REVERT: B  924 ASP cc_start: 0.8615 (m-30) cc_final: 0.8383 (m-30)
REVERT: B 1048 MET cc_start: 0.8908 (mtm) cc_final: 0.8601 (mtp)
  outliers start: 15
  outliers final: 8
  residues processed: 82
  average time/residue: 1.8872
  time to fit residues: 169.4542
Evaluate side-chains
  76 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  922 THR
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue  922 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 113 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 140 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 124 optimal weight:    0.8980
   chunk 141 optimal weight:    0.0770
   chunk 29 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.085409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.061171 restraints weight = 22640.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.74
r_work: 0.2650 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2517 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12622  Z= 0.124
  Angle     :  0.492  11.768  17054  Z= 0.258
  Chirality :  0.041   0.186   1848
  Planarity :  0.004   0.047   2176
  Dihedral  :  4.231  24.021   1684
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.31 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.22), residues: 1510
  helix:  1.36 (0.21), residues: 688
  sheet: -0.71 (0.38), residues: 190
  loop : -0.13 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.000   HIS A1051 
 PHE   0.010   0.001   PHE A 990 
 TYR   0.033   0.001   TYR A1122 
 ARG   0.015   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  558)
  hydrogen bonds       : angle       4.16127 ( 1572)
  covalent geometry    : bond        0.00284 (12622)
  covalent geometry    : angle       0.49222 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8974 (mmmt)
REVERT: A  924 ASP cc_start: 0.8558 (m-30) cc_final: 0.8343 (m-30)
REVERT: A  988 GLU cc_start: 0.8646 (pt0) cc_final: 0.8280 (pp20)
REVERT: A 1048 MET cc_start: 0.8885 (mtm) cc_final: 0.8584 (mtp)
REVERT: A 1087 ARG cc_start: 0.7855 (ptm-80) cc_final: 0.7573 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8967 (mt0) cc_final: 0.8651 (mm110)
REVERT: B  660 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7744 (ttp-170)
REVERT: B  924 ASP cc_start: 0.8549 (m-30) cc_final: 0.8312 (m-30)
REVERT: B 1048 MET cc_start: 0.8873 (mtm) cc_final: 0.8562 (mtp)
REVERT: B 1160 GLN cc_start: 0.8961 (mt0) cc_final: 0.8655 (mm110)
  outliers start: 11
  outliers final: 7
  residues processed: 85
  average time/residue: 1.6098
  time to fit residues: 148.5923
Evaluate side-chains
  84 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 1.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue  922 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 136 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 61 optimal weight:    0.3980
   chunk 108 optimal weight:    1.9990
   chunk 139 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 146 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 864 GLN
A1099 HIS
B 864 GLN
B1099 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.085214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.060815 restraints weight = 22560.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.74
r_work: 0.2638 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2505 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12622  Z= 0.131
  Angle     :  0.498  11.193  17054  Z= 0.261
  Chirality :  0.042   0.187   1848
  Planarity :  0.004   0.051   2176
  Dihedral  :  4.239  24.091   1684
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  9.91 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1510
  helix:  1.37 (0.21), residues: 690
  sheet: -0.70 (0.38), residues: 190
  loop : -0.13 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1099 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.032   0.001   TYR B1122 
 ARG   0.015   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  558)
  hydrogen bonds       : angle       4.15422 ( 1572)
  covalent geometry    : bond        0.00305 (12622)
  covalent geometry    : angle       0.49830 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 1.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8976 (mmmt)
REVERT: A  924 ASP cc_start: 0.8547 (m-30) cc_final: 0.8314 (m-30)
REVERT: A  988 GLU cc_start: 0.8635 (pt0) cc_final: 0.8299 (pp20)
REVERT: A 1048 MET cc_start: 0.8879 (mtm) cc_final: 0.8582 (mtp)
REVERT: A 1087 ARG cc_start: 0.7836 (ptm-80) cc_final: 0.7535 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8974 (mt0) cc_final: 0.8655 (mm110)
REVERT: B  454 LYS cc_start: 0.9209 (mtmm) cc_final: 0.9009 (mmmt)
REVERT: B  924 ASP cc_start: 0.8537 (m-30) cc_final: 0.8303 (m-30)
REVERT: B 1048 MET cc_start: 0.8879 (mtm) cc_final: 0.8574 (mtp)
REVERT: B 1160 GLN cc_start: 0.8972 (mt0) cc_final: 0.8661 (mm110)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 1.6527
  time to fit residues: 148.2240
Evaluate side-chains
  79 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 143 optimal weight:    0.1980
   chunk 99 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0980
   chunk 59 optimal weight:    0.5980
   chunk 144 optimal weight:    0.2980
   chunk 75 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0570
   overall best weight:    0.2498

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.087828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.063780 restraints weight = 22254.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.72
r_work: 0.2702 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2572 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12622  Z= 0.096
  Angle     :  0.485  11.335  17054  Z= 0.252
  Chirality :  0.040   0.167   1848
  Planarity :  0.004   0.053   2176
  Dihedral  :  4.001  22.459   1684
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.21 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.23), residues: 1510
  helix:  1.54 (0.21), residues: 680
  sheet: -0.59 (0.38), residues: 190
  loop : -0.24 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 820 
 HIS   0.003   0.000   HIS B1099 
 PHE   0.011   0.001   PHE B 990 
 TYR   0.035   0.001   TYR A1122 
 ARG   0.015   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02990 (  558)
  hydrogen bonds       : angle       4.07274 ( 1572)
  covalent geometry    : bond        0.00206 (12622)
  covalent geometry    : angle       0.48505 (17054)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 2.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9195 (mtmm) cc_final: 0.8981 (mmmt)
REVERT: A  924 ASP cc_start: 0.8518 (m-30) cc_final: 0.8108 (m-30)
REVERT: A  988 GLU cc_start: 0.8610 (pt0) cc_final: 0.8278 (pp20)
REVERT: A 1041 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8647 (mm-30)
REVERT: A 1048 MET cc_start: 0.8860 (mtm) cc_final: 0.8555 (mtp)
REVERT: A 1087 ARG cc_start: 0.7821 (ptm-80) cc_final: 0.7567 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8900 (mt0) cc_final: 0.8594 (mm110)
REVERT: B  662 ARG cc_start: 0.8491 (mpp80) cc_final: 0.7853 (mpp80)
REVERT: B  924 ASP cc_start: 0.8519 (m-30) cc_final: 0.8117 (m-30)
REVERT: B 1041 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8636 (mm-30)
REVERT: B 1048 MET cc_start: 0.8860 (mtm) cc_final: 0.8549 (mtp)
REVERT: B 1160 GLN cc_start: 0.8953 (mt0) cc_final: 0.8658 (mm110)
  outliers start: 6
  outliers final: 4
  residues processed: 85
  average time/residue: 2.1015
  time to fit residues: 194.2617
Evaluate side-chains
  82 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 127 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 139 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3272 r_free = 0.3272 target = 0.085686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.061258 restraints weight = 22279.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 2.73
r_work: 0.2648 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2517 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12622  Z= 0.132
  Angle     :  0.502  11.111  17054  Z= 0.263
  Chirality :  0.041   0.166   1848
  Planarity :  0.004   0.055   2176
  Dihedral  :  4.119  23.387   1684
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 10.06 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.23), residues: 1510
  helix:  1.57 (0.21), residues: 676
  sheet: -0.63 (0.39), residues: 190
  loop : -0.22 (0.26), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.031   0.001   TYR B1122 
 ARG   0.015   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (  558)
  hydrogen bonds       : angle       4.10629 ( 1572)
  covalent geometry    : bond        0.00310 (12622)
  covalent geometry    : angle       0.50158 (17054)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9738.67 seconds
wall clock time: 173 minutes 40.37 seconds (10420.37 seconds total)