Starting phenix.real_space_refine
on Sat Aug 23 11:37:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8c_36067/08_2025/8j8c_36067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8c_36067/08_2025/8j8c_36067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8c_36067/08_2025/8j8c_36067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8c_36067/08_2025/8j8c_36067.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8c_36067/08_2025/8j8c_36067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8c_36067/08_2025/8j8c_36067.map"
  }
  resolution = 2.69
  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=   0.009
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    7492      2.51       5
     N    2004      2.21       5
     O    2104      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 11650
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 717, 5825
          Classifications: {'peptide': 717}
          Link IDs: {'PTRANS': 28, 'TRANS': 688}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 717, 5825
          Classifications: {'peptide': 717}
          Link IDs: {'PTRANS': 28, 'TRANS': 688}
          Chain breaks: 3
  Time building chain proxies: 2.45, per 1000 atoms: 0.21
  Number of scatterers: 11650
  At special positions: 0
  Unit cell: (108.73, 107.9, 105.41, 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    2104      8.00
     N    2004      7.00
     C    7492      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: 0.84
  Conformation dependent library (CDL) restraints added in 423.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 16 sheets defined
      48.3% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  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 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: 3.972A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.535A  pdb=" N   PHE A 596 " --> pdb=" O   TYR A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
      removed outlier: 3.535A  pdb=" N   HIS A 620 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.629A  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: 3.863A  pdb=" N   LYS A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU A 647 " --> pdb=" O   ASP A 643 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   HIS A 650 " --> pdb=" O   LYS A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 664
      removed outlier: 3.921A  pdb=" N   LYS A 661 " --> pdb=" O   SER A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 682
    Processing helix  chain 'A' and resid 687 through 705
      removed outlier: 3.628A  pdb=" N   THR A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 4.546A  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 767
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.756A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 877
    Processing helix  chain 'A' and resid 882 through 893
      removed outlier: 3.941A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 3.764A  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: 3.983A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLU A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU A 989 " --> pdb=" O   ARG A 985 " (cutoff:3.500A)
      removed outlier: 3.522A  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 1068
      removed outlier: 3.692A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1109 through 1119
    Processing helix  chain 'A' and resid 1137 through 1158
    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 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: 3.973A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 602
      removed outlier: 3.534A  pdb=" N   PHE B 596 " --> pdb=" O   TYR B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
      removed outlier: 3.537A  pdb=" N   HIS B 620 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.629A  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: 3.863A  pdb=" N   LYS B 646 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU B 647 " --> pdb=" O   ASP B 643 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   HIS B 650 " --> pdb=" O   LYS B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 664
      removed outlier: 3.921A  pdb=" N   LYS B 661 " --> pdb=" O   SER B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 682
    Processing helix  chain 'B' and resid 687 through 705
      removed outlier: 3.626A  pdb=" N   THR B 695 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.546A  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 767
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 3.756A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 866 through 877
    Processing helix  chain 'B' and resid 882 through 893
      removed outlier: 3.941A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (cutoff:3.500A)
      removed outlier: 3.764A  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: 3.983A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLU B 988 " --> pdb=" O   ASN B 984 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU B 989 " --> pdb=" O   ARG B 985 " (cutoff:3.500A)
      removed outlier: 3.523A  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 1068
      removed outlier: 3.692A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1109 through 1119
    Processing helix  chain 'B' and resid 1137 through 1158
    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: 6.103A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   ILE A 685 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 6.079A  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: 3.575A  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: 4.464A  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: 5.852A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU A 975 " --> pdb=" O   ILE A 963 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 963 " --> pdb=" O   LEU A 975 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   LYS A 977 " --> pdb=" O   GLU A 961 " (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: 6.102A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 6.080A  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: 3.575A  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: 4.465A  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: 5.851A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B 975 " --> pdb=" O   ILE B 963 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE B 963 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   LYS B 977 " --> pdb=" O   GLU B 961 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016

    528 hydrogen bonds defined for protein.
    1500 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: 1.72

  Time building geometry restraints manager: 1.07 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: 3746
        1.34 -     1.46: 2716
        1.46 -     1.58: 5384
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 11924
  Sorted by residual:
  bond pdb=" C   SER A1162 "
       pdb=" N   PRO A1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.18e-01
  bond pdb=" CB  ILE A 801 "
       pdb=" CG2 ILE A 801 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.11e-01
  bond pdb=" CB  ILE B 801 "
       pdb=" CG2 ILE B 801 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.83e-01
  bond pdb=" C   SER B1162 "
       pdb=" N   PRO B1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.68e-01
  bond pdb=" N   ASN B 732 "
       pdb=" CA  ASN B 732 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.29e-02 6.01e+03 5.91e-01
  ... (remaining 11919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 15966
        1.78 -     3.56: 114
        3.56 -     5.34: 18
        5.34 -     7.12: 0
        7.12 -     8.90: 2
  Bond angle restraints: 16100
  Sorted by residual:
  angle pdb=" N   ILE A 845 "
        pdb=" CA  ILE A 845 "
        pdb=" C   ILE A 845 "
      ideal   model   delta    sigma   weight residual
     112.96  109.38    3.58 1.00e+00 1.00e+00 1.28e+01
  angle pdb=" N   ILE B 845 "
        pdb=" CA  ILE B 845 "
        pdb=" C   ILE B 845 "
      ideal   model   delta    sigma   weight residual
     112.96  109.39    3.57 1.00e+00 1.00e+00 1.27e+01
  angle pdb=" CA  LEU A1159 "
        pdb=" CB  LEU A1159 "
        pdb=" CG  LEU A1159 "
      ideal   model   delta    sigma   weight residual
     116.30  125.20   -8.90 3.50e+00 8.16e-02 6.47e+00
  angle pdb=" CA  LEU B1159 "
        pdb=" CB  LEU B1159 "
        pdb=" CG  LEU B1159 "
      ideal   model   delta    sigma   weight residual
     116.30  125.19   -8.89 3.50e+00 8.16e-02 6.45e+00
  angle pdb=" N   LYS B 991 "
        pdb=" CA  LYS B 991 "
        pdb=" CB  LYS B 991 "
      ideal   model   delta    sigma   weight residual
     113.65  109.93    3.72 1.47e+00 4.63e-01 6.40e+00
  ... (remaining 16095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.56: 6589
       10.56 -    21.12: 400
       21.12 -    31.67: 125
       31.67 -    42.23: 20
       42.23 -    52.79: 12
  Dihedral angle restraints: 7146
    sinusoidal: 2952
      harmonic: 4194
  Sorted by residual:
  dihedral pdb=" CA  SER A 731 "
           pdb=" C   SER A 731 "
           pdb=" N   ASN A 732 "
           pdb=" CA  ASN A 732 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.03   27.97     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  SER B 731 "
           pdb=" C   SER B 731 "
           pdb=" N   ASN B 732 "
           pdb=" CA  ASN B 732 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.13   27.87     0      5.00e+00 4.00e-02 3.11e+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 -162.01  -17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 7143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1044
       0.026 -    0.051: 396
       0.051 -    0.077: 193
       0.077 -    0.103: 66
       0.103 -    0.128: 43
  Chirality restraints: 1742
  Sorted by residual:
  chirality pdb=" CA  ILE A 685 "
            pdb=" N   ILE A 685 "
            pdb=" C   ILE A 685 "
            pdb=" CB  ILE A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-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   -0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  ILE B 707 "
            pdb=" N   ILE B 707 "
            pdb=" C   ILE B 707 "
            pdb=" CB  ILE B 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 1739 not shown)

  Planarity restraints: 2048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 937 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO A 938 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.06e+00
        pdb=" N   PRO B 938 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B1164 "   -0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO B1165 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B1165 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B1165 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 2045 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2468
        2.78 -     3.31: 11011
        3.31 -     3.84: 18886
        3.84 -     4.37: 23500
        4.37 -     4.90: 40102
  Nonbonded interactions: 95967
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B1043 "
            pdb=" OE1 GLU B1173 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OH  TYR A1043 "
            pdb=" OE1 GLU A1173 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG  SER B 919 "
            pdb=" ND2 ASN B1007 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OG  SER B 787 "
            pdb=" OD2 ASP B 794 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER A 787 "
            pdb=" OD2 ASP A 794 "
     model   vdw
     2.286 3.040
  ... (remaining 95962 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: 0.01
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
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   0.028  11924  Z= 0.102
  Angle     :  0.416   8.903  16100  Z= 0.225
  Chirality :  0.039   0.128   1742
  Planarity :  0.003   0.044   2048
  Dihedral  :  8.078  52.788   4458
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  2.15 %
    Favored  : 97.37 %
  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:  0.89 (0.23), residues: 1418
  helix:  1.28 (0.21), residues: 626
  sheet:  0.10 (0.42), residues: 178
  loop :  0.17 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 863 
 TYR   0.006   0.001   TYR A 837 
 PHE   0.008   0.001   PHE A 990 
 TRP   0.004   0.001   TRP B 856 
 HIS   0.002   0.000   HIS A1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (11924)
  covalent geometry    : angle       0.41588 (16100)
  hydrogen bonds       : bond        0.24008 (  528)
  hydrogen bonds       : angle       6.22139 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 ARG cc_start: 0.8168 (mmp-170) cc_final: 0.7940 (mmp-170)
REVERT: A  714 MET cc_start: 0.9088 (ptp) cc_final: 0.8862 (ptp)
REVERT: A  846 MET cc_start: 0.8910 (mtm) cc_final: 0.8709 (mtp)
REVERT: A 1060 MET cc_start: 0.8047 (ttt) cc_final: 0.7617 (tpt)
REVERT: A 1148 MET cc_start: 0.8463 (ptp) cc_final: 0.8184 (ptt)
REVERT: B  433 MET cc_start: 0.8082 (ptp) cc_final: 0.7811 (ptp)
REVERT: B  662 ARG cc_start: 0.8113 (mmp-170) cc_final: 0.7899 (mmp-170)
REVERT: B  714 MET cc_start: 0.9055 (ptp) cc_final: 0.8798 (ptp)
REVERT: B  846 MET cc_start: 0.8928 (mtm) cc_final: 0.8716 (mtp)
REVERT: B  988 GLU cc_start: 0.8633 (tt0) cc_final: 0.8404 (mm-30)
  outliers start: 6
  outliers final: 2
  residues processed: 121
  average time/residue: 0.7898
  time to fit residues: 101.1212
Evaluate side-chains
  64 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain B residue  549 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1051 HIS
B1007 ASN
B1051 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.087185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.064752 restraints weight = 23671.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 3.12
r_work: 0.2825 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11924  Z= 0.141
  Angle     :  0.508   9.992  16100  Z= 0.271
  Chirality :  0.042   0.139   1742
  Planarity :  0.004   0.045   2048
  Dihedral  :  4.315  53.007   1592
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  5.41 %
    Favored  : 92.75 %
  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:  1.05 (0.23), residues: 1418
  helix:  1.52 (0.21), residues: 642
  sheet: -0.01 (0.41), residues: 186
  loop :  0.13 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 929 
 TYR   0.012   0.001   TYR A 555 
 PHE   0.014   0.001   PHE B 990 
 TRP   0.006   0.001   TRP B1189 
 HIS   0.004   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11924)
  covalent geometry    : angle       0.50772 (16100)
  hydrogen bonds       : bond        0.04608 (  528)
  hydrogen bonds       : angle       4.47728 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8924 (ptp) cc_final: 0.8676 (ptp)
REVERT: A  846 MET cc_start: 0.9093 (mtm) cc_final: 0.8880 (mtp)
REVERT: A 1060 MET cc_start: 0.7800 (ttt) cc_final: 0.7393 (tpt)
REVERT: B  714 MET cc_start: 0.8919 (ptp) cc_final: 0.8656 (ptp)
REVERT: B  846 MET cc_start: 0.9107 (mtm) cc_final: 0.8906 (mtp)
REVERT: B  988 GLU cc_start: 0.8988 (tt0) cc_final: 0.8611 (mm-30)
REVERT: B 1147 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8335 (mtmm)
  outliers start: 23
  outliers final: 4
  residues processed: 83
  average time/residue: 0.5896
  time to fit residues: 52.7909
Evaluate side-chains
  62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 33 optimal weight:    0.0050
   chunk 46 optimal weight:    0.0770
   chunk 96 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0870
   chunk 51 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 135 optimal weight:    6.9990
   chunk 10 optimal weight:    0.1980
   chunk 45 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.2330

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.089253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.067298 restraints weight = 23649.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 3.11
r_work: 0.2879 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  11924  Z= 0.095
  Angle     :  0.460  10.185  16100  Z= 0.241
  Chirality :  0.040   0.142   1742
  Planarity :  0.003   0.044   2048
  Dihedral  :  4.179  52.999   1592
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  6.45 %
    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 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 (0.23), residues: 1418
  helix:  1.58 (0.21), residues: 644
  sheet:  0.01 (0.40), residues: 188
  loop :  0.03 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 929 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.000   HIS A1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 (11924)
  covalent geometry    : angle       0.45965 (16100)
  hydrogen bonds       : bond        0.03359 (  528)
  hydrogen bonds       : angle       4.08937 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8853 (ptp) cc_final: 0.8587 (ptp)
REVERT: A 1060 MET cc_start: 0.7809 (ttt) cc_final: 0.7352 (tpt)
REVERT: A 1149 GLN cc_start: 0.8973 (tp40) cc_final: 0.8734 (tp-100)
REVERT: B  549 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8383 (tt)
REVERT: B  658 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7562 (pp20)
REVERT: B  714 MET cc_start: 0.8826 (ptp) cc_final: 0.8549 (ptp)
REVERT: B  846 MET cc_start: 0.9072 (mtm) cc_final: 0.8853 (mtp)
REVERT: B  988 GLU cc_start: 0.8987 (tt0) cc_final: 0.8594 (mm-30)
REVERT: B 1103 ILE cc_start: 0.7212 (pp) cc_final: 0.6949 (pp)
REVERT: B 1147 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8352 (mtmm)
  outliers start: 19
  outliers final: 4
  residues processed: 81
  average time/residue: 0.6136
  time to fit residues: 53.8430
Evaluate side-chains
  71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 118 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 49 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 135 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3369 r_free = 0.3369 target = 0.087091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.064903 restraints weight = 23683.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 3.12
r_work: 0.2833 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11924  Z= 0.127
  Angle     :  0.477  10.381  16100  Z= 0.248
  Chirality :  0.041   0.137   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.279  52.616   1592
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.09 %
    Favored  : 91.56 %
  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:  0.97 (0.23), residues: 1418
  helix:  1.58 (0.21), residues: 644
  sheet: -0.30 (0.39), residues: 192
  loop :  0.03 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 929 
 TYR   0.012   0.001   TYR A 920 
 PHE   0.013   0.001   PHE B 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (11924)
  covalent geometry    : angle       0.47677 (16100)
  hydrogen bonds       : bond        0.03287 (  528)
  hydrogen bonds       : angle       3.97947 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8664 (pp20)
REVERT: A  606 LEU cc_start: 0.9361 (mt) cc_final: 0.9029 (mm)
REVERT: A  658 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7754 (tm-30)
REVERT: A  659 LEU cc_start: 0.8127 (mm) cc_final: 0.7797 (mt)
REVERT: A  714 MET cc_start: 0.8849 (ptp) cc_final: 0.8571 (ptp)
REVERT: A  784 SER cc_start: 0.8706 (m) cc_final: 0.8490 (t)
REVERT: A 1060 MET cc_start: 0.7813 (ttt) cc_final: 0.7354 (tpt)
REVERT: B  524 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8689 (pp20)
REVERT: B  658 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7611 (pp20)
REVERT: B  714 MET cc_start: 0.8825 (ptp) cc_final: 0.8566 (ptp)
REVERT: B 1103 ILE cc_start: 0.7235 (pp) cc_final: 0.7031 (pp)
REVERT: B 1147 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (mtmm)
  outliers start: 17
  outliers final: 5
  residues processed: 83
  average time/residue: 0.6215
  time to fit residues: 55.5409
Evaluate side-chains
  70 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 126 optimal weight:    0.0470
   chunk 45 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 71 optimal weight:    0.1980
   chunk 73 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.087454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.065384 restraints weight = 23747.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 3.10
r_work: 0.2843 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11924  Z= 0.110
  Angle     :  0.468  10.462  16100  Z= 0.243
  Chirality :  0.041   0.134   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.267  52.435   1592
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.88 %
    Favored  : 90.84 %
  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:  0.97 (0.23), residues: 1418
  helix:  1.61 (0.21), residues: 644
  sheet: -0.36 (0.39), residues: 192
  loop :  0.02 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 929 
 TYR   0.012   0.001   TYR A 920 
 PHE   0.012   0.001   PHE B 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (11924)
  covalent geometry    : angle       0.46833 (16100)
  hydrogen bonds       : bond        0.03043 (  528)
  hydrogen bonds       : angle       3.91010 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8669 (pp20)
REVERT: A  606 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9023 (mm)
REVERT: A  659 LEU cc_start: 0.8090 (mm) cc_final: 0.7879 (mt)
REVERT: A  714 MET cc_start: 0.8871 (ptp) cc_final: 0.8621 (ptp)
REVERT: A  784 SER cc_start: 0.8667 (m) cc_final: 0.8461 (t)
REVERT: A 1060 MET cc_start: 0.7832 (ttt) cc_final: 0.7363 (tpt)
REVERT: B  658 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7594 (pp20)
REVERT: B  714 MET cc_start: 0.8877 (ptp) cc_final: 0.8621 (ptp)
REVERT: B 1147 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8345 (mtmm)
  outliers start: 16
  outliers final: 6
  residues processed: 73
  average time/residue: 0.7052
  time to fit residues: 55.3375
Evaluate side-chains
  71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  887 HIS
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue  887 HIS
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 98 optimal weight:    0.3980
   chunk 132 optimal weight:    1.9990
   chunk 137 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 136 optimal weight:    3.9990
   chunk 107 optimal weight:    0.2980
   chunk 93 optimal weight:    0.0070
   chunk 97 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4198

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.088259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.066260 restraints weight = 23670.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 3.12
r_work: 0.2860 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
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      :  0.002   0.030  11924  Z= 0.098
  Angle     :  0.461  10.736  16100  Z= 0.238
  Chirality :  0.040   0.135   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.180  52.183   1592
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.80 %
    Favored  : 90.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.23), residues: 1418
  helix:  1.61 (0.21), residues: 644
  sheet: -0.20 (0.40), residues: 188
  loop : -0.03 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 929 
 TYR   0.012   0.001   TYR A 920 
 PHE   0.012   0.001   PHE B 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.004   0.000   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (11924)
  covalent geometry    : angle       0.46075 (16100)
  hydrogen bonds       : bond        0.02846 (  528)
  hydrogen bonds       : angle       3.85269 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8666 (pp20)
REVERT: A  606 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9018 (mm)
REVERT: A  658 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7774 (tm-30)
REVERT: A  659 LEU cc_start: 0.8058 (mm) cc_final: 0.7852 (mt)
REVERT: A  714 MET cc_start: 0.8877 (ptp) cc_final: 0.8608 (ptp)
REVERT: A 1060 MET cc_start: 0.7873 (ttt) cc_final: 0.7339 (tpt)
REVERT: A 1103 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6990 (tp)
REVERT: B  524 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8675 (pp20)
REVERT: B  658 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7592 (pp20)
REVERT: B  714 MET cc_start: 0.8873 (ptp) cc_final: 0.8609 (ptp)
  outliers start: 18
  outliers final: 6
  residues processed: 84
  average time/residue: 0.6633
  time to fit residues: 60.1825
Evaluate side-chains
  72 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  887 HIS
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0170
   chunk 90 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.5818

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.087476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.065429 restraints weight = 23739.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 3.11
r_work: 0.2842 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11924  Z= 0.114
  Angle     :  0.477  10.837  16100  Z= 0.247
  Chirality :  0.041   0.134   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.230  52.062   1592
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.00 %
    Favored  : 89.65 %
  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:  0.96 (0.23), residues: 1418
  helix:  1.60 (0.21), residues: 646
  sheet: -0.34 (0.39), residues: 192
  loop : -0.00 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 929 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.008   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (11924)
  covalent geometry    : angle       0.47676 (16100)
  hydrogen bonds       : bond        0.02883 (  528)
  hydrogen bonds       : angle       3.85891 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8668 (pp20)
REVERT: A  606 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9040 (mm)
REVERT: A  658 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7778 (tm-30)
REVERT: A  659 LEU cc_start: 0.8121 (mm) cc_final: 0.7897 (mt)
REVERT: A  714 MET cc_start: 0.8875 (ptp) cc_final: 0.8620 (ptp)
REVERT: A 1060 MET cc_start: 0.7852 (ttt) cc_final: 0.7333 (tpt)
REVERT: A 1103 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7082 (tp)
REVERT: A 1149 GLN cc_start: 0.8991 (tp40) cc_final: 0.8707 (tp-100)
REVERT: B  524 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8683 (pp20)
REVERT: B  658 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7588 (pp20)
REVERT: B  692 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7952 (pt0)
REVERT: B  714 MET cc_start: 0.8872 (ptp) cc_final: 0.8613 (ptp)
REVERT: B 1048 MET cc_start: 0.8107 (mtm) cc_final: 0.7211 (mtm)
  outliers start: 17
  outliers final: 6
  residues processed: 75
  average time/residue: 0.7831
  time to fit residues: 63.0395
Evaluate side-chains
  73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  887 HIS
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 123 optimal weight:    0.4980
   chunk 89 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0470
   overall best weight:    0.5678

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.087433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.065524 restraints weight = 23643.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 3.08
r_work: 0.2843 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11924  Z= 0.112
  Angle     :  0.485  11.030  16100  Z= 0.248
  Chirality :  0.041   0.134   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.236  51.955   1592
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.24 %
    Favored  : 89.57 %
  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:  0.96 (0.23), residues: 1418
  helix:  1.60 (0.21), residues: 646
  sheet: -0.33 (0.39), residues: 192
  loop : -0.00 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 929 
 TYR   0.018   0.001   TYR A1122 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.009   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (11924)
  covalent geometry    : angle       0.48522 (16100)
  hydrogen bonds       : bond        0.02855 (  528)
  hydrogen bonds       : angle       3.84529 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8672 (pp20)
REVERT: A  606 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9023 (mm)
REVERT: A  658 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7222 (tm-30)
REVERT: A  692 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7949 (pt0)
REVERT: A  714 MET cc_start: 0.8883 (ptp) cc_final: 0.8628 (ptp)
REVERT: A 1042 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8913 (tt)
REVERT: A 1048 MET cc_start: 0.8027 (mtm) cc_final: 0.7246 (mtm)
REVERT: A 1060 MET cc_start: 0.7836 (ttt) cc_final: 0.7323 (tpt)
REVERT: A 1103 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7053 (tp)
REVERT: A 1149 GLN cc_start: 0.8994 (tp40) cc_final: 0.8706 (tp-100)
REVERT: B  524 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8676 (pp20)
REVERT: B  607 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9125 (m)
REVERT: B  658 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7583 (pp20)
REVERT: B  692 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7929 (pt0)
REVERT: B  714 MET cc_start: 0.8878 (ptp) cc_final: 0.8621 (ptp)
REVERT: B  735 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8543 (mt-10)
REVERT: B 1048 MET cc_start: 0.8064 (mtm) cc_final: 0.7109 (mtm)
  outliers start: 15
  outliers final: 5
  residues processed: 75
  average time/residue: 0.7510
  time to fit residues: 60.2461
Evaluate side-chains
  76 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  887 HIS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 126 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 139 optimal weight:    0.9990
   chunk 131 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 83 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.6782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.086891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.064918 restraints weight = 23598.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.08
r_work: 0.2830 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11924  Z= 0.123
  Angle     :  0.495  11.044  16100  Z= 0.253
  Chirality :  0.041   0.137   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.291  52.005   1592
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.16 %
    Favored  : 89.65 %
  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:  0.96 (0.23), residues: 1418
  helix:  1.59 (0.21), residues: 646
  sheet: -0.34 (0.39), residues: 192
  loop :  0.00 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 929 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.005   0.001   TRP A1189 
 HIS   0.010   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (11924)
  covalent geometry    : angle       0.49478 (16100)
  hydrogen bonds       : bond        0.02922 (  528)
  hydrogen bonds       : angle       3.85919 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8665 (pp20)
REVERT: A  606 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9037 (mm)
REVERT: A  692 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7954 (pt0)
REVERT: A  714 MET cc_start: 0.8878 (ptp) cc_final: 0.8646 (ptp)
REVERT: A 1042 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8877 (tt)
REVERT: A 1060 MET cc_start: 0.7820 (ttt) cc_final: 0.7314 (tpt)
REVERT: A 1099 HIS cc_start: 0.6918 (t70) cc_final: 0.6654 (t-170)
REVERT: A 1103 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7022 (tp)
REVERT: A 1122 TYR cc_start: 0.4556 (t80) cc_final: 0.4047 (t80)
REVERT: A 1149 GLN cc_start: 0.8990 (tp40) cc_final: 0.8689 (tp-100)
REVERT: B  524 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8666 (pp20)
REVERT: B  607 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9157 (m)
REVERT: B  658 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7576 (pp20)
REVERT: B  692 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7939 (pt0)
REVERT: B  714 MET cc_start: 0.8870 (ptp) cc_final: 0.8638 (ptp)
REVERT: B 1048 MET cc_start: 0.8087 (mtm) cc_final: 0.7162 (mtm)
  outliers start: 15
  outliers final: 4
  residues processed: 77
  average time/residue: 0.6951
  time to fit residues: 57.4869
Evaluate side-chains
  73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 118 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 139 optimal weight:    0.0000
   chunk 50 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
B 887 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.087100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.065118 restraints weight = 23832.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.10
r_work: 0.2839 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11924  Z= 0.115
  Angle     :  0.503  11.257  16100  Z= 0.255
  Chirality :  0.041   0.138   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.278  51.973   1592
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.47 %
    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:  0.99 (0.23), residues: 1418
  helix:  1.63 (0.21), residues: 646
  sheet: -0.34 (0.39), residues: 192
  loop :  0.02 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 929 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (11924)
  covalent geometry    : angle       0.50312 (16100)
  hydrogen bonds       : bond        0.02876 (  528)
  hydrogen bonds       : angle       3.86151 ( 1500)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8666 (pp20)
REVERT: A  606 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9018 (mm)
REVERT: A  607 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9180 (m)
REVERT: A  692 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7955 (pt0)
REVERT: A  714 MET cc_start: 0.8878 (ptp) cc_final: 0.8623 (ptp)
REVERT: A 1042 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8850 (tt)
REVERT: A 1060 MET cc_start: 0.7808 (ttt) cc_final: 0.7318 (tpt)
REVERT: A 1103 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7065 (tp)
REVERT: A 1122 TYR cc_start: 0.4255 (t80) cc_final: 0.3750 (t80)
REVERT: A 1149 GLN cc_start: 0.8983 (tp40) cc_final: 0.8682 (tp-100)
REVERT: B  524 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8663 (pp20)
REVERT: B  607 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9156 (m)
REVERT: B  658 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7579 (pp20)
REVERT: B  692 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7948 (pt0)
REVERT: B  714 MET cc_start: 0.8867 (ptp) cc_final: 0.8609 (ptp)
REVERT: B 1048 MET cc_start: 0.7988 (mtm) cc_final: 0.7059 (mtm)
  outliers start: 13
  outliers final: 3
  residues processed: 71
  average time/residue: 0.7193
  time to fit residues: 54.8241
Evaluate side-chains
  73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1103 ILE
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  658 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 85 optimal weight:    0.1980
   chunk 91 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 140 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 117 optimal weight:    0.3980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3369 r_free = 0.3369 target = 0.087195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.065320 restraints weight = 23717.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 3.10
r_work: 0.2841 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11924  Z= 0.113
  Angle     :  0.501  11.221  16100  Z= 0.255
  Chirality :  0.041   0.134   1742
  Planarity :  0.004   0.046   2048
  Dihedral  :  4.274  51.962   1592
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.55 %
    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:  0.98 (0.23), residues: 1418
  helix:  1.62 (0.21), residues: 646
  sheet: -0.48 (0.39), residues: 196
  loop :  0.07 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 929 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11924)
  covalent geometry    : angle       0.50087 (16100)
  hydrogen bonds       : bond        0.02855 (  528)
  hydrogen bonds       : angle       3.86732 ( 1500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2865.94 seconds
wall clock time: 49 minutes 47.47 seconds (2987.47 seconds total)