Starting phenix.real_space_refine
on Wed Jul 30 00:00:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8c_36067/07_2025/8j8c_36067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8c_36067/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8c_36067/07_2025/8j8c_36067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8c_36067/07_2025/8j8c_36067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8c_36067/07_2025/8j8c_36067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8c_36067/07_2025/8j8c_36067.cif"
  }
  resolution = 2.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.94, per 1000 atoms: 0.68
  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.46
  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: 3.95

  Time building geometry restraints manager: 3.28 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.100
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.300
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (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
 TRP   0.004   0.001   TRP B 856 
 HIS   0.002   0.000   HIS A1051 
 PHE   0.008   0.001   PHE A 990 
 TYR   0.006   0.001   TYR A 837 
 ARG   0.003   0.000   ARG A 863 

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

*********************** 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  : 1.299 
Fit side-chains
   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: 0.7890 (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: 0.7844 (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: 0.8717 (mtp)
REVERT: B  988 GLU cc_start: 0.8633 (tt0) cc_final: 0.8404 (mm-30)
REVERT: B 1041 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7856 (mm-30)
  outliers start: 6
  outliers final: 2
  residues processed: 121
  average time/residue: 2.0379
  time to fit residues: 261.7042
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  : 2.127 
-------------------------------------------------------------------------------
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 119 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 128 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:
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 = 0.3352 r_free = 0.3352 target = 0.085960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.063402 restraints weight = 23569.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.13
r_work: 0.2783 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11924  Z= 0.178
  Angle     :  0.528   9.936  16100  Z= 0.282
  Chirality :  0.043   0.142   1742
  Planarity :  0.004   0.044   2048
  Dihedral  :  4.466  52.833   1592
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  5.10 %
    Favored  : 92.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.23), residues: 1418
  helix:  1.47 (0.21), residues: 640
  sheet: -0.09 (0.41), residues: 186
  loop :  0.10 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.005   0.001   HIS B1051 
 PHE   0.015   0.001   PHE B 990 
 TYR   0.013   0.001   TYR A 555 
 ARG   0.005   0.000   ARG A 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04453 (  528)
  hydrogen bonds       : angle       4.44747 ( 1500)
  covalent geometry    : bond        0.00415 (11924)
  covalent geometry    : angle       0.52837 (16100)

*********************** 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
  92 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  658 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7416 (tm-30)
REVERT: A  714 MET cc_start: 0.8862 (ptp) cc_final: 0.8642 (ptp)
REVERT: A  846 MET cc_start: 0.9125 (mtm) cc_final: 0.8913 (mtp)
REVERT: A 1060 MET cc_start: 0.7807 (ttt) cc_final: 0.7393 (tpt)
REVERT: B  714 MET cc_start: 0.8863 (ptp) cc_final: 0.8634 (ptp)
REVERT: B  846 MET cc_start: 0.9128 (mtm) cc_final: 0.8901 (mtp)
REVERT: B  988 GLU cc_start: 0.8996 (tt0) cc_final: 0.8619 (mm-30)
REVERT: B 1147 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8371 (mtmm)
  outliers start: 24
  outliers final: 5
  residues processed: 84
  average time/residue: 2.1132
  time to fit residues: 192.3018
Evaluate side-chains
  63 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 126 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 94 optimal weight:    0.2980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3362 r_free = 0.3362 target = 0.086694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.064486 restraints weight = 23868.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 3.12
r_work: 0.2823 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1905

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= 0.119
  Angle     :  0.479  10.047  16100  Z= 0.253
  Chirality :  0.041   0.137   1742
  Planarity :  0.003   0.044   2048
  Dihedral  :  4.403  52.782   1592
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  6.21 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.23), residues: 1418
  helix:  1.53 (0.21), residues: 640
  sheet: -0.22 (0.40), residues: 192
  loop :  0.03 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.013   0.001   PHE A 990 
 TYR   0.012   0.001   TYR A1122 
 ARG   0.008   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  528)
  hydrogen bonds       : angle       4.15541 ( 1500)
  covalent geometry    : bond        0.00270 (11924)
  covalent geometry    : angle       0.47901 (16100)

*********************** 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
  84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 2.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8638 (pp20)
REVERT: A  606 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9026 (mm)
REVERT: A  714 MET cc_start: 0.8837 (ptp) cc_final: 0.8602 (ptp)
REVERT: A  846 MET cc_start: 0.9119 (mtm) cc_final: 0.8912 (mtp)
REVERT: A 1060 MET cc_start: 0.7803 (ttt) cc_final: 0.7380 (tpt)
REVERT: B  714 MET cc_start: 0.8828 (ptp) cc_final: 0.8578 (ptp)
REVERT: B  846 MET cc_start: 0.9130 (mtm) cc_final: 0.8910 (mtp)
REVERT: B 1103 ILE cc_start: 0.7215 (pp) cc_final: 0.6974 (pp)
REVERT: B 1147 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8400 (mtmm)
  outliers start: 22
  outliers final: 6
  residues processed: 76
  average time/residue: 2.1217
  time to fit residues: 173.5656
Evaluate side-chains
  66 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 1.781 
-------------------------------------------------------------------------------
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 B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 138 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 10 optimal weight:    0.7980
   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 = 0.3361 r_free = 0.3361 target = 0.086526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.064191 restraints weight = 23413.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.11
r_work: 0.2817 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2120

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     :  0.484  10.269  16100  Z= 0.251
  Chirality :  0.041   0.137   1742
  Planarity :  0.004   0.046   2048
  Dihedral  :  4.386  52.497   1592
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  6.77 %
    Favored  : 91.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.23), residues: 1418
  helix:  1.54 (0.21), residues: 644
  sheet: -0.36 (0.39), residues: 192
  loop : -0.03 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1051 
 PHE   0.013   0.001   PHE A 990 
 TYR   0.012   0.001   TYR A 920 
 ARG   0.008   0.000   ARG A 662 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  528)
  hydrogen bonds       : angle       4.03516 ( 1500)
  covalent geometry    : bond        0.00293 (11924)
  covalent geometry    : angle       0.48396 (16100)

*********************** 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
  83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 1.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8644 (pp20)
REVERT: A  606 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9029 (mm)
REVERT: A  659 LEU cc_start: 0.8072 (mm) cc_final: 0.7736 (mt)
REVERT: A  662 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7289 (ttp80)
REVERT: A  714 MET cc_start: 0.8828 (ptp) cc_final: 0.8579 (ptp)
REVERT: A  846 MET cc_start: 0.9116 (mtm) cc_final: 0.8909 (mtp)
REVERT: A 1060 MET cc_start: 0.7822 (ttt) cc_final: 0.7385 (tpt)
REVERT: B  524 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8676 (pp20)
REVERT: B  658 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7812 (tm-30)
REVERT: B  659 LEU cc_start: 0.8115 (mm) cc_final: 0.7802 (mt)
REVERT: B  662 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7300 (ttp80)
REVERT: B  714 MET cc_start: 0.8836 (ptp) cc_final: 0.8583 (ptp)
REVERT: B  846 MET cc_start: 0.9113 (mtm) cc_final: 0.8885 (mtp)
REVERT: B 1103 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7014 (pp)
REVERT: B 1147 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8363 (mtmm)
  outliers start: 20
  outliers final: 6
  residues processed: 76
  average time/residue: 1.7328
  time to fit residues: 142.1638
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  : 1.426 
-------------------------------------------------------------------------------
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 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 1103 ILE
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0770
   chunk 68 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0270
   chunk 89 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.2174

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.088901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.067148 restraints weight = 23495.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 3.09
r_work: 0.2880 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11924  Z= 0.087
  Angle     :  0.460  10.631  16100  Z= 0.237
  Chirality :  0.040   0.137   1742
  Planarity :  0.003   0.045   2048
  Dihedral  :  4.160  52.312   1592
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  7.56 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.23), residues: 1418
  helix:  1.59 (0.21), residues: 646
  sheet: -0.18 (0.40), residues: 188
  loop : -0.07 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.003   0.000   HIS A1051 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.012   0.001   TYR B1122 
 ARG   0.009   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02775 (  528)
  hydrogen bonds       : angle       3.87708 ( 1500)
  covalent geometry    : bond        0.00185 (11924)
  covalent geometry    : angle       0.45997 (16100)

*********************** 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
  89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  549 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8410 (tt)
REVERT: A  606 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9007 (mm)
REVERT: A  659 LEU cc_start: 0.8077 (mm) cc_final: 0.7742 (mt)
REVERT: A  662 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7401 (ttp80)
REVERT: A  714 MET cc_start: 0.8809 (ptp) cc_final: 0.8541 (ptp)
REVERT: A 1060 MET cc_start: 0.7813 (ttt) cc_final: 0.7319 (tpt)
REVERT: B  549 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8427 (tt)
REVERT: B  659 LEU cc_start: 0.8109 (mm) cc_final: 0.7712 (mt)
REVERT: B  662 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7303 (ttp80)
REVERT: B  714 MET cc_start: 0.8812 (ptp) cc_final: 0.8537 (ptp)
REVERT: B 1048 MET cc_start: 0.8025 (mtp) cc_final: 0.7670 (mtm)
REVERT: B 1103 ILE cc_start: 0.7239 (pp) cc_final: 0.7031 (pp)
REVERT: B 1147 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8362 (mtmm)
  outliers start: 19
  outliers final: 4
  residues processed: 83
  average time/residue: 1.3582
  time to fit residues: 122.8920
Evaluate side-chains
  70 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  549 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  887 HIS
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0870
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.2562

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

Flipped N/Q/H residues before XYZ refinement:
A 887 HIS
** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 887 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.084529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.062170 restraints weight = 23904.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 3.12
r_work: 0.2772 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11924  Z= 0.193
  Angle     :  0.521  10.576  16100  Z= 0.273
  Chirality :  0.043   0.143   1742
  Planarity :  0.004   0.047   2048
  Dihedral  :  4.578  52.329   1592
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.28 %
    Favored  : 90.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.23), residues: 1418
  helix:  1.54 (0.21), residues: 640
  sheet: -0.69 (0.38), residues: 196
  loop : -0.03 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1170 
 HIS   0.003   0.001   HIS B1051 
 PHE   0.014   0.001   PHE B 990 
 TYR   0.013   0.001   TYR A 555 
 ARG   0.010   0.001   ARG A 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  528)
  hydrogen bonds       : angle       4.03812 ( 1500)
  covalent geometry    : bond        0.00458 (11924)
  covalent geometry    : angle       0.52099 (16100)

*********************** 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
  81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 1.328 
Fit side-chains
REVERT: A  524 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8646 (pp20)
REVERT: A  606 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9061 (mm)
REVERT: A  658 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7738 (tm-30)
REVERT: A  659 LEU cc_start: 0.8140 (mm) cc_final: 0.7791 (mt)
REVERT: A  714 MET cc_start: 0.8860 (ptp) cc_final: 0.8647 (ptp)
REVERT: A 1060 MET cc_start: 0.7832 (ttt) cc_final: 0.7349 (tpt)
REVERT: B  524 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8676 (pp20)
REVERT: B  659 LEU cc_start: 0.8139 (mm) cc_final: 0.7843 (mt)
REVERT: B  714 MET cc_start: 0.8850 (ptp) cc_final: 0.8642 (ptp)
REVERT: B  735 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8620 (mt-10)
REVERT: B 1103 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7078 (pp)
REVERT: B 1147 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8380 (mtmm)
  outliers start: 21
  outliers final: 7
  residues processed: 73
  average time/residue: 1.4545
  time to fit residues: 115.0336
Evaluate side-chains
  70 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
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 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  735 GLU
Chi-restraints excluded: chain B residue  960 ILE
Chi-restraints excluded: chain B residue 1103 ILE
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Chi-restraints excluded: chain B residue 1159 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0970
   chunk 66 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 105 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.086300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.064106 restraints weight = 23863.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.12
r_work: 0.2814 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2403

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= 0.115
  Angle     :  0.488  10.845  16100  Z= 0.250
  Chirality :  0.041   0.134   1742
  Planarity :  0.003   0.045   2048
  Dihedral  :  4.403  52.052   1592
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.00 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.23), residues: 1418
  helix:  1.59 (0.21), residues: 644
  sheet: -0.63 (0.39), residues: 196
  loop : -0.03 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.003   0.001   HIS B1051 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.017   0.001   TYR A1122 
 ARG   0.009   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02987 (  528)
  hydrogen bonds       : angle       3.92112 ( 1500)
  covalent geometry    : bond        0.00264 (11924)
  covalent geometry    : angle       0.48771 (16100)

*********************** 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: 16
    poor density    : 61
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  606 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9036 (mm)
REVERT: A  658 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7762 (tm-30)
REVERT: A  659 LEU cc_start: 0.8066 (mm) cc_final: 0.7830 (mt)
REVERT: A 1060 MET cc_start: 0.7795 (ttt) cc_final: 0.7347 (tpt)
REVERT: B  524 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8659 (pp20)
REVERT: B  607 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9173 (m)
REVERT: B  659 LEU cc_start: 0.8166 (mm) cc_final: 0.7858 (mt)
REVERT: B  662 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7264 (ttp80)
REVERT: B  714 MET cc_start: 0.8859 (ptp) cc_final: 0.8625 (ptp)
REVERT: B 1103 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7104 (pp)
REVERT: B 1147 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8373 (mtmm)
  outliers start: 16
  outliers final: 4
  residues processed: 71
  average time/residue: 1.5479
  time to fit residues: 118.6629
Evaluate side-chains
  69 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 1103 ILE
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 60 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 141 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 120 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5336

-------------------------------------------------------------------------------
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 = 0.3364 r_free = 0.3364 target = 0.086868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.064828 restraints weight = 23745.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 3.12
r_work: 0.2821 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2459

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= 0.111
  Angle     :  0.488  11.092  16100  Z= 0.250
  Chirality :  0.041   0.134   1742
  Planarity :  0.003   0.046   2048
  Dihedral  :  4.316  51.890   1592
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.84 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.23), residues: 1418
  helix:  1.62 (0.21), residues: 646
  sheet: -0.61 (0.39), residues: 196
  loop :  0.01 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.006   0.001   HIS A1099 
 PHE   0.012   0.001   PHE B 990 
 TYR   0.011   0.001   TYR A 920 
 ARG   0.010   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02895 (  528)
  hydrogen bonds       : angle       3.87618 ( 1500)
  covalent geometry    : bond        0.00254 (11924)
  covalent geometry    : angle       0.48848 (16100)

*********************** 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
  83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 1.483 
Fit side-chains
   revert: symmetry clash
REVERT: A  606 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9022 (mm)
REVERT: A  658 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7761 (tm-30)
REVERT: A  659 LEU cc_start: 0.8085 (mm) cc_final: 0.7808 (mt)
REVERT: A  692 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7886 (pt0)
REVERT: A  735 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8585 (mt-10)
REVERT: A 1042 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8874 (tt)
REVERT: A 1060 MET cc_start: 0.7852 (ttt) cc_final: 0.7346 (tpt)
REVERT: B  524 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8659 (pp20)
REVERT: B  607 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9177 (m)
REVERT: B  659 LEU cc_start: 0.8076 (mm) cc_final: 0.7857 (mt)
REVERT: B  662 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7299 (ttp-110)
REVERT: B  692 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7868 (pt0)
REVERT: B  714 MET cc_start: 0.8850 (ptp) cc_final: 0.8615 (ptp)
REVERT: B 1103 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7139 (pp)
REVERT: B 1147 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8378 (mtmm)
  outliers start: 18
  outliers final: 5
  residues processed: 76
  average time/residue: 1.5458
  time to fit residues: 126.9540
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  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  735 GLU
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue 1042 LEU
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 1103 ILE
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   chunk 39 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3364 r_free = 0.3364 target = 0.086881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.064838 restraints weight = 23647.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 3.13
r_work: 0.2811 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11924  Z= 0.109
  Angle     :  0.500  11.386  16100  Z= 0.253
  Chirality :  0.041   0.135   1742
  Planarity :  0.004   0.046   2048
  Dihedral  :  4.305  51.851   1592
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1418
  helix:  1.63 (0.21), residues: 646
  sheet: -0.60 (0.39), residues: 196
  loop :  0.03 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.010   0.001   HIS A1099 
 PHE   0.012   0.001   PHE B 990 
 TYR   0.020   0.001   TYR A1122 
 ARG   0.010   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02872 (  528)
  hydrogen bonds       : angle       3.86159 ( 1500)
  covalent geometry    : bond        0.00250 (11924)
  covalent geometry    : angle       0.49995 (16100)

*********************** 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
  81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 1.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  606 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9004 (mm)
REVERT: A  607 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9171 (m)
REVERT: A  658 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7787 (tm-30)
REVERT: A  692 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7876 (pt0)
REVERT: A 1042 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8759 (tt)
REVERT: A 1060 MET cc_start: 0.7801 (ttt) cc_final: 0.7324 (tpt)
REVERT: A 1122 TYR cc_start: 0.4698 (t80) cc_final: 0.4486 (t80)
REVERT: B  524 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8660 (pp20)
REVERT: B  607 VAL cc_start: 0.9389 (OUTLIER) cc_final: 0.9167 (m)
REVERT: B  658 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7807 (tm-30)
REVERT: B  659 LEU cc_start: 0.8073 (mm) cc_final: 0.7773 (mt)
REVERT: B  662 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7309 (ttp-110)
REVERT: B  692 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7846 (pt0)
REVERT: B  714 MET cc_start: 0.8813 (ptp) cc_final: 0.8572 (ptp)
REVERT: B 1042 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8870 (tt)
REVERT: B 1048 MET cc_start: 0.8096 (mtp) cc_final: 0.7671 (mtm)
REVERT: B 1122 TYR cc_start: 0.4742 (t80) cc_final: 0.4272 (t80)
REVERT: B 1147 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (mtmm)
  outliers start: 16
  outliers final: 4
  residues processed: 75
  average time/residue: 1.7674
  time to fit residues: 142.8693
Evaluate side-chains
  77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  960 ILE
Chi-restraints excluded: chain A residue 1042 LEU
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 1042 LEU
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 55 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0010
   chunk 92 optimal weight:    3.9990
   chunk 133 optimal weight:    3.9990
   chunk 132 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.086760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.064770 restraints weight = 23586.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 3.11
r_work: 0.2826 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11924  Z= 0.115
  Angle     :  0.509  11.344  16100  Z= 0.259
  Chirality :  0.041   0.134   1742
  Planarity :  0.004   0.046   2048
  Dihedral  :  4.314  51.775   1592
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1418
  helix:  1.61 (0.21), residues: 646
  sheet: -0.60 (0.39), residues: 196
  loop :  0.05 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.012   0.001   HIS A1099 
 PHE   0.012   0.001   PHE B 990 
 TYR   0.018   0.001   TYR A1122 
 ARG   0.010   0.000   ARG B 929 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02868 (  528)
  hydrogen bonds       : angle       3.86413 ( 1500)
  covalent geometry    : bond        0.00265 (11924)
  covalent geometry    : angle       0.50893 (16100)

********************** 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
  78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  606 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9002 (mm)
REVERT: A  607 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9171 (m)
REVERT: A  659 LEU cc_start: 0.8123 (mt) cc_final: 0.7873 (mt)
REVERT: A  692 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7896 (pt0)
REVERT: A 1042 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8794 (tt)
REVERT: A 1060 MET cc_start: 0.7809 (ttt) cc_final: 0.7332 (tpt)
REVERT: A 1122 TYR cc_start: 0.4653 (t80) cc_final: 0.4433 (t80)
REVERT: B  524 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8656 (pp20)
REVERT: B  607 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9203 (m)
REVERT: B  658 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7806 (tm-30)
REVERT: B  659 LEU cc_start: 0.8098 (mm) cc_final: 0.7860 (mt)
REVERT: B  692 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7876 (pt0)
REVERT: B  714 MET cc_start: 0.8851 (ptp) cc_final: 0.8623 (ptp)
REVERT: B 1042 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8853 (tt)
REVERT: B 1147 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8371 (mtmm)
  outliers start: 14
  outliers final: 4
  residues processed: 72
  average time/residue: 1.5809
  time to fit residues: 122.8231
Evaluate side-chains
  74 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  960 ILE
Chi-restraints excluded: chain A residue 1042 LEU
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 1042 LEU
Chi-restraints excluded: chain B residue 1147 LYS
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 101 optimal weight:    0.2980
   chunk 72 optimal weight:    4.9990
   chunk 120 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 117 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 112 optimal weight:    0.0670
   chunk 17 optimal weight:    0.4980
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.4118

-------------------------------------------------------------------------------
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 = 0.3376 r_free = 0.3376 target = 0.087507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.065591 restraints weight = 23510.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.12
r_work: 0.2844 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11924  Z= 0.102
  Angle     :  0.505  11.471  16100  Z= 0.255
  Chirality :  0.041   0.162   1742
  Planarity :  0.004   0.046   2048
  Dihedral  :  4.242  51.697   1592
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.79 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1418
  helix:  1.59 (0.21), residues: 646
  sheet: -0.58 (0.39), residues: 196
  loop :  0.06 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.012   0.001   HIS A1099 
 PHE   0.012   0.001   PHE B 990 
 TYR   0.018   0.001   TYR A1122 
 ARG   0.010   0.000   ARG A 662 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02791 (  528)
  hydrogen bonds       : angle       3.84017 ( 1500)
  covalent geometry    : bond        0.00230 (11924)
  covalent geometry    : angle       0.50469 (16100)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7869.99 seconds
wall clock time: 141 minutes 41.40 seconds (8501.40 seconds total)