Starting phenix.real_space_refine
on Sat Aug 23 13:49:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8b_36066/08_2025/8j8b_36066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8b_36066/08_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_36066/08_2025/8j8b_36066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8b_36066/08_2025/8j8b_36066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8b_36066/08_2025/8j8b_36066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8b_36066/08_2025/8j8b_36066.cif"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.42, per 1000 atoms: 0.36
  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: 0.78
  Conformation dependent library (CDL) restraints added in 475.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.41
  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: 1.87

  Time building geometry restraints manager: 1.09 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: 0.02
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:             4.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.350
  Find NCS groups from input model:        0.090
  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:8.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.090
-------------------------------------------------------------------------------
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 : 5.60
  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 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:  1.04 (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
 ARG   0.010   0.000   ARG A 734 
 TYR   0.022   0.001   TYR A1122 
 PHE   0.007   0.001   PHE B 990 
 TRP   0.004   0.001   TRP A 820 
 HIS   0.004   0.001   HIS B1078 

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

*********************** 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  : 0.403 
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: 0.6358
  time to fit residues: 72.1364
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  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.083721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.059108 restraints weight = 22760.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 2.72
r_work: 0.2607 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2475 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  12622  Z= 0.264
  Angle     :  0.582   7.483  17054  Z= 0.316
  Chirality :  0.046   0.153   1848
  Planarity :  0.005   0.071   2176
  Dihedral  :  4.407  24.181   1684
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.11 %
    Favored  : 94.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.22), residues: 1510
  helix:  1.07 (0.20), residues: 690
  sheet: -0.15 (0.39), residues: 180
  loop :  0.00 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 734 
 TYR   0.028   0.002   TYR B1122 
 PHE   0.012   0.002   PHE A 462 
 TRP   0.007   0.002   TRP A 856 
 HIS   0.004   0.001   HIS A1012 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (12622)
  covalent geometry    : angle       0.58231 (17054)
  hydrogen bonds       : bond        0.05506 (  558)
  hydrogen bonds       : angle       4.71111 ( 1572)

*********************** 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  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  701 ASP cc_start: 0.8621 (t70) cc_final: 0.8368 (t70)
REVERT: A  915 GLN cc_start: 0.9150 (pt0) cc_final: 0.8900 (pt0)
REVERT: B  662 ARG cc_start: 0.8297 (mpp80) cc_final: 0.7767 (mpp80)
REVERT: B  701 ASP cc_start: 0.8562 (t70) cc_final: 0.8304 (t70)
REVERT: B  915 GLN cc_start: 0.9143 (pt0) cc_final: 0.8919 (pt0)
REVERT: B 1041 GLU cc_start: 0.8644 (pt0) cc_final: 0.8412 (mm-30)
REVERT: B 1143 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8246 (pp20)
  outliers start: 9
  outliers final: 5
  residues processed: 92
  average time/residue: 0.7410
  time to fit residues: 73.4027
Evaluate side-chains
  78 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  845 ILE
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 25 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 143 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 147 optimal weight:    2.9990
   chunk 116 optimal weight:    0.3980
   chunk 105 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0010
   chunk 106 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.4586

-------------------------------------------------------------------------------
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 = 0.3293 r_free = 0.3293 target = 0.086724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.062769 restraints weight = 22734.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 2.73
r_work: 0.2685 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12622  Z= 0.112
  Angle     :  0.499  15.335  17054  Z= 0.260
  Chirality :  0.041   0.134   1848
  Planarity :  0.004   0.044   2176
  Dihedral  :  4.139  21.949   1684
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.91 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.22), residues: 1510
  helix:  1.22 (0.20), residues: 690
  sheet: -0.57 (0.37), residues: 190
  loop :  0.02 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 734 
 TYR   0.026   0.001   TYR B1122 
 PHE   0.010   0.001   PHE B 990 
 TRP   0.007   0.001   TRP A 820 
 HIS   0.002   0.000   HIS A1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (12622)
  covalent geometry    : angle       0.49862 (17054)
  hydrogen bonds       : bond        0.03886 (  558)
  hydrogen bonds       : angle       4.43856 ( 1572)

*********************** 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
  95 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8969 (mtmm)
REVERT: A  662 ARG cc_start: 0.8547 (mpt-90) cc_final: 0.8154 (mpp80)
REVERT: A  915 GLN cc_start: 0.9149 (pt0) cc_final: 0.8933 (pt0)
REVERT: A  924 ASP cc_start: 0.8576 (m-30) cc_final: 0.8342 (m-30)
REVERT: A 1048 MET cc_start: 0.8889 (mtm) cc_final: 0.8586 (mtp)
REVERT: A 1087 ARG cc_start: 0.7941 (ptm-80) cc_final: 0.7603 (mtm-85)
REVERT: B  455 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8386 (t)
REVERT: B  662 ARG cc_start: 0.8318 (mpp80) cc_final: 0.7938 (mpp80)
REVERT: B  915 GLN cc_start: 0.9146 (pt0) cc_final: 0.8932 (pt0)
REVERT: B  924 ASP cc_start: 0.8585 (m-30) cc_final: 0.8359 (m-30)
REVERT: B 1143 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8208 (tm-30)
  outliers start: 11
  outliers final: 1
  residues processed: 90
  average time/residue: 0.8300
  time to fit residues: 80.2986
Evaluate side-chains
  71 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 SER
Chi-restraints excluded: chain B residue  586 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 145 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 83 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.085508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.060993 restraints weight = 22484.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 2.76
r_work: 0.2643 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2511 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12622  Z= 0.152
  Angle     :  0.503  12.594  17054  Z= 0.265
  Chirality :  0.042   0.136   1848
  Planarity :  0.004   0.054   2176
  Dihedral  :  4.237  22.920   1684
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.81 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.22), residues: 1510
  helix:  1.29 (0.20), residues: 690
  sheet: -0.66 (0.37), residues: 190
  loop : -0.03 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 734 
 TYR   0.026   0.001   TYR A1122 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1012 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (12622)
  covalent geometry    : angle       0.50263 (17054)
  hydrogen bonds       : bond        0.03878 (  558)
  hydrogen bonds       : angle       4.33853 ( 1572)

*********************** 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: 14
    poor density    : 77
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  662 ARG cc_start: 0.8585 (mpt-90) cc_final: 0.8081 (mpp80)
REVERT: A  915 GLN cc_start: 0.9165 (pt0) cc_final: 0.8927 (pt0)
REVERT: A  924 ASP cc_start: 0.8556 (m-30) cc_final: 0.8328 (m-30)
REVERT: A 1048 MET cc_start: 0.8897 (mtm) cc_final: 0.8579 (mtp)
REVERT: A 1087 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7576 (mtm-85)
REVERT: B  660 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7811 (ttp-170)
REVERT: B  915 GLN cc_start: 0.9149 (pt0) cc_final: 0.8935 (pt0)
REVERT: B  924 ASP cc_start: 0.8565 (m-30) cc_final: 0.8177 (m-30)
REVERT: B 1122 TYR cc_start: 0.6265 (t80) cc_final: 0.6040 (t80)
REVERT: B 1143 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8211 (tm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 85
  average time/residue: 0.7482
  time to fit residues: 68.8847
Evaluate side-chains
  77 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
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 1140 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 134 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 128 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   chunk 115 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 145 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.0784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.084362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.059840 restraints weight = 22715.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 2.72
r_work: 0.2622 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2489 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12622  Z= 0.179
  Angle     :  0.521  11.757  17054  Z= 0.275
  Chirality :  0.043   0.178   1848
  Planarity :  0.004   0.062   2176
  Dihedral  :  6.175 179.420   1684
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.41 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.22), residues: 1510
  helix:  1.26 (0.20), residues: 688
  sheet: -0.68 (0.37), residues: 190
  loop : -0.10 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 734 
 TYR   0.028   0.001   TYR A1122 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1012 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (12622)
  covalent geometry    : angle       0.52136 (17054)
  hydrogen bonds       : bond        0.03933 (  558)
  hydrogen bonds       : angle       4.30937 ( 1572)

*********************** 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: 15
    poor density    : 71
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  915 GLN cc_start: 0.9164 (pt0) cc_final: 0.8960 (pt0)
REVERT: A  924 ASP cc_start: 0.8569 (m-30) cc_final: 0.8336 (m-30)
REVERT: A 1048 MET cc_start: 0.8934 (mtm) cc_final: 0.8617 (mtp)
REVERT: A 1087 ARG cc_start: 0.7913 (ptm-80) cc_final: 0.7577 (mtm-85)
REVERT: B  915 GLN cc_start: 0.9153 (pt0) cc_final: 0.8952 (pt0)
REVERT: B  924 ASP cc_start: 0.8616 (m-30) cc_final: 0.8213 (m-30)
REVERT: B 1048 MET cc_start: 0.8941 (mtm) cc_final: 0.8607 (mtp)
REVERT: B 1143 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8184 (tm-30)
  outliers start: 15
  outliers final: 5
  residues processed: 83
  average time/residue: 0.7425
  time to fit residues: 66.7564
Evaluate side-chains
  72 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 134 optimal weight:    0.5980
   chunk 117 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.085124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.060748 restraints weight = 22478.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 2.71
r_work: 0.2643 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2511 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12622  Z= 0.140
  Angle     :  0.501  12.383  17054  Z= 0.263
  Chirality :  0.042   0.175   1848
  Planarity :  0.004   0.051   2176
  Dihedral  :  6.055 176.180   1684
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  8.93 %
    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 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 (0.22), residues: 1510
  helix:  1.33 (0.21), residues: 688
  sheet: -0.68 (0.38), residues: 190
  loop : -0.11 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 734 
 TYR   0.031   0.001   TYR A1122 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12622)
  covalent geometry    : angle       0.50064 (17054)
  hydrogen bonds       : bond        0.03601 (  558)
  hydrogen bonds       : angle       4.21924 ( 1572)

*********************** 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
  81 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  915 GLN cc_start: 0.9157 (pt0) cc_final: 0.8951 (pt0)
REVERT: A  924 ASP cc_start: 0.8562 (m-30) cc_final: 0.8316 (m-30)
REVERT: A  988 GLU cc_start: 0.8643 (pt0) cc_final: 0.8301 (pp20)
REVERT: A 1041 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8627 (mm-30)
REVERT: A 1048 MET cc_start: 0.8917 (mtm) cc_final: 0.8617 (mtp)
REVERT: A 1087 ARG cc_start: 0.7880 (ptm-80) cc_final: 0.7534 (mtm-85)
REVERT: B  454 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8993 (mtmm)
REVERT: B  662 ARG cc_start: 0.8447 (mpp80) cc_final: 0.7760 (mpp80)
REVERT: B  915 GLN cc_start: 0.9157 (pt0) cc_final: 0.8943 (pt0)
REVERT: B  924 ASP cc_start: 0.8567 (m-30) cc_final: 0.8154 (m-30)
REVERT: B 1048 MET cc_start: 0.8900 (mtm) cc_final: 0.8591 (mtp)
  outliers start: 6
  outliers final: 4
  residues processed: 79
  average time/residue: 0.8027
  time to fit residues: 68.4653
Evaluate side-chains
  76 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 132 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0050
   chunk 67 optimal weight:    0.0270
   chunk 96 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5052

-------------------------------------------------------------------------------
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 = 0.3280 r_free = 0.3280 target = 0.086121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.061913 restraints weight = 22411.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 2.70
r_work: 0.2667 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2535 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12622  Z= 0.114
  Angle     :  0.488  11.545  17054  Z= 0.256
  Chirality :  0.041   0.197   1848
  Planarity :  0.004   0.080   2176
  Dihedral  :  5.885 171.136   1684
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.93 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.22), residues: 1510
  helix:  1.38 (0.21), residues: 690
  sheet: -0.67 (0.38), residues: 190
  loop : -0.08 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B1140 
 TYR   0.034   0.001   TYR A1122 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.000   HIS B1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12622)
  covalent geometry    : angle       0.48829 (17054)
  hydrogen bonds       : bond        0.03358 (  558)
  hydrogen bonds       : angle       4.13578 ( 1572)

*********************** 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
  94 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  915 GLN cc_start: 0.9155 (pt0) cc_final: 0.8951 (pt0)
REVERT: A  924 ASP cc_start: 0.8562 (m-30) cc_final: 0.8321 (m-30)
REVERT: A  988 GLU cc_start: 0.8623 (pt0) cc_final: 0.8295 (pp20)
REVERT: A 1041 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8625 (mm-30)
REVERT: A 1048 MET cc_start: 0.8906 (mtm) cc_final: 0.8605 (mtp)
REVERT: A 1087 ARG cc_start: 0.7872 (ptm-80) cc_final: 0.7538 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8958 (mt0) cc_final: 0.8695 (mm-40)
REVERT: B  662 ARG cc_start: 0.8466 (mpp80) cc_final: 0.7792 (mpp80)
REVERT: B  915 GLN cc_start: 0.9159 (pt0) cc_final: 0.8957 (pt0)
REVERT: B  924 ASP cc_start: 0.8541 (m-30) cc_final: 0.8313 (m-30)
REVERT: B 1048 MET cc_start: 0.8886 (mtm) cc_final: 0.8583 (mtp)
REVERT: B 1140 ARG cc_start: 0.8288 (mtm110) cc_final: 0.8072 (mtm110)
  outliers start: 13
  outliers final: 6
  residues processed: 88
  average time/residue: 0.8308
  time to fit residues: 78.7969
Evaluate side-chains
  83 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 118 optimal weight:    0.9980
   chunk 125 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 124 optimal weight:    0.6980
   chunk 148 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 864 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.085200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.060813 restraints weight = 22550.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 2.70
r_work: 0.2639 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2507 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12622  Z= 0.138
  Angle     :  0.498  11.204  17054  Z= 0.261
  Chirality :  0.042   0.183   1848
  Planarity :  0.004   0.051   2176
  Dihedral  :  5.991 174.670   1684
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.38 %
    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 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:  0.68 (0.22), residues: 1510
  helix:  1.41 (0.21), residues: 690
  sheet: -0.76 (0.38), residues: 190
  loop : -0.11 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 734 
 TYR   0.032   0.001   TYR A1122 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12622)
  covalent geometry    : angle       0.49753 (17054)
  hydrogen bonds       : bond        0.03501 (  558)
  hydrogen bonds       : angle       4.15688 ( 1572)

*********************** 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: 10
    poor density    : 81
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  915 GLN cc_start: 0.9165 (pt0) cc_final: 0.8953 (pt0)
REVERT: A  924 ASP cc_start: 0.8582 (m-30) cc_final: 0.8346 (m-30)
REVERT: A  988 GLU cc_start: 0.8626 (pt0) cc_final: 0.8322 (pp20)
REVERT: A 1048 MET cc_start: 0.8923 (mtm) cc_final: 0.8623 (mtp)
REVERT: A 1087 ARG cc_start: 0.7854 (ptm-80) cc_final: 0.7552 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8977 (mt0) cc_final: 0.8707 (mm-40)
REVERT: B  915 GLN cc_start: 0.9164 (pt0) cc_final: 0.8958 (pt0)
REVERT: B  924 ASP cc_start: 0.8583 (m-30) cc_final: 0.8340 (m-30)
REVERT: B 1048 MET cc_start: 0.8913 (mtm) cc_final: 0.8609 (mtp)
REVERT: B 1140 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7989 (mtm110)
REVERT: B 1160 GLN cc_start: 0.8974 (mt0) cc_final: 0.8710 (mm-40)
  outliers start: 10
  outliers final: 7
  residues processed: 88
  average time/residue: 0.8089
  time to fit residues: 76.6120
Evaluate side-chains
  81 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
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  735 GLU
Chi-restraints excluded: chain B residue  803 VAL
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 110 optimal weight:    3.9990
   chunk 149 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0060
   chunk 121 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 126 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.3283 r_free = 0.3283 target = 0.086372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.062258 restraints weight = 22335.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 2.72
r_work: 0.2668 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2537 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12622  Z= 0.111
  Angle     :  0.489  11.387  17054  Z= 0.255
  Chirality :  0.041   0.178   1848
  Planarity :  0.004   0.052   2176
  Dihedral  :  5.914 174.715   1684
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.83 %
    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 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:  0.74 (0.23), residues: 1510
  helix:  1.44 (0.21), residues: 688
  sheet: -0.67 (0.38), residues: 190
  loop : -0.08 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG B 734 
 TYR   0.034   0.001   TYR A1122 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A 820 
 HIS   0.003   0.000   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (12622)
  covalent geometry    : angle       0.48931 (17054)
  hydrogen bonds       : bond        0.03228 (  558)
  hydrogen bonds       : angle       4.08820 ( 1572)

*********************** 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: 10
    poor density    : 76
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8937 (mmmt)
REVERT: A  915 GLN cc_start: 0.9154 (pt0) cc_final: 0.8952 (pt0)
REVERT: A  924 ASP cc_start: 0.8537 (m-30) cc_final: 0.8296 (m-30)
REVERT: A  988 GLU cc_start: 0.8639 (pt0) cc_final: 0.8318 (pp20)
REVERT: A 1048 MET cc_start: 0.8879 (mtm) cc_final: 0.8588 (mtp)
REVERT: A 1087 ARG cc_start: 0.7794 (ptm-80) cc_final: 0.7538 (mtm-85)
REVERT: A 1160 GLN cc_start: 0.8973 (mt0) cc_final: 0.8706 (mm-40)
REVERT: B  915 GLN cc_start: 0.9165 (pt0) cc_final: 0.8951 (pt0)
REVERT: B  924 ASP cc_start: 0.8534 (m-30) cc_final: 0.8127 (m-30)
REVERT: B 1048 MET cc_start: 0.8864 (mtm) cc_final: 0.8571 (mtp)
REVERT: B 1140 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7796 (mtm110)
REVERT: B 1160 GLN cc_start: 0.8938 (mt0) cc_final: 0.8680 (mm-40)
  outliers start: 10
  outliers final: 5
  residues processed: 83
  average time/residue: 0.7280
  time to fit residues: 65.4852
Evaluate side-chains
  80 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  735 GLU
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 96 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 101 optimal weight:    1.9990
   chunk 140 optimal weight:    0.5980
   chunk 110 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0370
   overall best weight:    1.1264

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

Flipped N/Q/H residues before XYZ refinement:
A 709 ASN
B 709 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.083704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.059191 restraints weight = 22695.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 2.72
r_work: 0.2602 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2469 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12622  Z= 0.187
  Angle     :  0.536  10.889  17054  Z= 0.283
  Chirality :  0.043   0.197   1848
  Planarity :  0.005   0.061   2176
  Dihedral  :  6.118 175.063   1684
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.06 %
    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 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 (0.23), residues: 1510
  helix:  1.34 (0.21), residues: 690
  sheet: -0.73 (0.38), residues: 190
  loop : -0.12 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 734 
 TYR   0.030   0.001   TYR A1122 
 PHE   0.013   0.001   PHE A 990 
 TRP   0.007   0.001   TRP B 861 
 HIS   0.003   0.001   HIS B 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12622)
  covalent geometry    : angle       0.53642 (17054)
  hydrogen bonds       : bond        0.03808 (  558)
  hydrogen bonds       : angle       4.22170 ( 1572)

********************** 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
  76 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8923 (mmmt)
REVERT: A  659 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8013 (mm)
REVERT: A  662 ARG cc_start: 0.8659 (mpt-90) cc_final: 0.8241 (mpp80)
REVERT: A  924 ASP cc_start: 0.8592 (m-30) cc_final: 0.8176 (m-30)
REVERT: A  988 GLU cc_start: 0.8674 (pt0) cc_final: 0.8349 (pp20)
REVERT: A 1048 MET cc_start: 0.8908 (mtm) cc_final: 0.8609 (mtp)
REVERT: A 1087 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7539 (mtm-85)
REVERT: B  846 MET cc_start: 0.8973 (mtp) cc_final: 0.8759 (mtp)
REVERT: B  924 ASP cc_start: 0.8594 (m-30) cc_final: 0.8183 (m-30)
REVERT: B 1048 MET cc_start: 0.8898 (mtm) cc_final: 0.8597 (mtp)
REVERT: B 1160 GLN cc_start: 0.8993 (mt0) cc_final: 0.8776 (mp10)
  outliers start: 6
  outliers final: 4
  residues processed: 75
  average time/residue: 0.7683
  time to fit residues: 62.2904
Evaluate side-chains
  71 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  659 LEU
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:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 148 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0010
   chunk 130 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.5986

-------------------------------------------------------------------------------
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 = 0.3267 r_free = 0.3267 target = 0.085494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.061079 restraints weight = 22459.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 2.74
r_work: 0.2642 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2510 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12622  Z= 0.125
  Angle     :  0.505  11.446  17054  Z= 0.264
  Chirality :  0.041   0.201   1848
  Planarity :  0.004   0.067   2176
  Dihedral  :  5.967 172.659   1684
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 10.44 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.23), residues: 1510
  helix:  1.38 (0.21), residues: 690
  sheet: -0.68 (0.38), residues: 190
  loop : -0.11 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 734 
 TYR   0.034   0.001   TYR A1122 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A 820 
 HIS   0.003   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12622)
  covalent geometry    : angle       0.50484 (17054)
  hydrogen bonds       : bond        0.03379 (  558)
  hydrogen bonds       : angle       4.14151 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4324.92 seconds
wall clock time: 74 minutes 47.20 seconds (4487.20 seconds total)