Starting phenix.real_space_refine
on Sat Oct 11 06:23:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j89_36064/10_2025/8j89_36064.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j89_36064/10_2025/8j89_36064.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j89_36064/10_2025/8j89_36064.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j89_36064/10_2025/8j89_36064.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j89_36064/10_2025/8j89_36064.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j89_36064/10_2025/8j89_36064.map"
  }
  resolution = 2.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    7855      2.51       5
     N    2097      2.21       5
     O    2220      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12222
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 751, 6105
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 30, 'TRANS': 720}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6117
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 751, 6105
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 30, 'TRANS': 720}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 751, 6105
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 30, 'TRANS': 720}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 6237
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR B1029 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR B1029 " occ=0.50
  Time building chain proxies: 3.92, per 1000 atoms: 0.32
  Number of scatterers: 12222
  At special positions: 0
  Unit cell: (115.37, 103.75, 111.22, 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    2220      8.00
     N    2097      7.00
     C    7855      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: 1.08
  Conformation dependent library (CDL) restraints added in 877.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2826

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 14 sheets defined
      51.7% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  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: 3.923A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.709A  pdb=" N   LYS A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.566A  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 644 through 653
    Processing helix  chain 'A' and resid 659 through 664
      removed outlier: 3.707A  pdb=" N   GLU A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 682
      removed outlier: 3.523A  pdb=" N   VAL A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 705
      removed outlier: 3.524A  pdb=" N   THR A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   LYS A 696 " --> pdb=" O   GLN A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 738 through 749
    Processing helix  chain 'A' and resid 754 through 765
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.676A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 847
      removed outlier: 3.505A  pdb=" N   MET A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 842 through 847'
    Processing helix  chain 'A' and resid 864 through 877
    Processing helix  chain 'A' and resid 882 through 891
      removed outlier: 3.839A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (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: 3.718A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
      removed outlier: 3.658A  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 1071
      removed outlier: 3.735A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1075 through 1079
    Processing helix  chain 'A' and resid 1081 through 1092
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1118
      removed outlier: 4.541A  pdb=" N   LEU A1118 " --> pdb=" O   ASN A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1127
    Processing helix  chain 'A' and resid 1129 through 1133
    Processing helix  chain 'A' and resid 1134 through 1160
    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: 3.927A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 602
      removed outlier: 3.757A  pdb=" N   LYS B 602 " --> pdb=" O   ALA B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.607A  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 644 through 653
      removed outlier: 3.596A  pdb=" N   HIS B 650 " --> pdb=" O   LYS B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 664
      removed outlier: 3.517A  pdb=" N   GLU B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 682
      removed outlier: 3.518A  pdb=" N   VAL B 682 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 692
    Processing helix  chain 'B' and resid 693 through 705
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 738 through 749
    Processing helix  chain 'B' and resid 754 through 765
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 3.669A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 847
      removed outlier: 3.545A  pdb=" N   MET B 846 " --> pdb=" O   PRO B 842 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLU B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 842 through 847'
    Processing helix  chain 'B' and resid 864 through 877
    Processing helix  chain 'B' and resid 882 through 891
      removed outlier: 3.860A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (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: 3.684A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU B 988 " --> pdb=" O   ASN B 984 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1071
      removed outlier: 3.721A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1075 through 1079
    Processing helix  chain 'B' and resid 1081 through 1092
    Processing helix  chain 'B' and resid 1098 through 1104
    Processing helix  chain 'B' and resid 1109 through 1118
      removed outlier: 4.554A  pdb=" N   LEU B1118 " --> pdb=" O   ASN B1114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1122 through 1127
    Processing helix  chain 'B' and resid 1129 through 1133
    Processing helix  chain 'B' and resid 1134 through 1160
    Processing helix  chain 'B' and resid 1166 through 1187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469
      removed outlier: 6.279A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.789A  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: 8.013A  pdb=" N   ILE A 685 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 6.244A  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
    Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.514A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 909 through 913
    Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 926
      removed outlier: 5.876A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU A 962 " --> pdb=" O   LYS A 977 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1013 through 1016
      removed outlier: 4.454A  pdb=" N   LEU A1013 " --> pdb=" O   PHE A1025 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 465 through 469
      removed outlier: 6.170A  pdb=" N   LEU B 434 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   CYS B 537 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA B 436 " --> pdb=" O   CYS B 537 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   THR B 638 " --> pdb=" O   ILE B 685 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737
    Processing sheet with id=AB2, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.487A  pdb=" N   VAL B 825 " --> pdb=" O   ALA B 832 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 909 through 913
    Processing sheet with id=AB4, first strand: chain 'B' and resid 922 through 926
      removed outlier: 5.867A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU B 962 " --> pdb=" O   LYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1014 through 1016

    566 hydrogen bonds defined for protein.
    1590 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: 2.32

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3943
        1.35 -     1.46: 2969
        1.46 -     1.58: 5526
        1.58 -     1.70: 0
        1.70 -     1.81: 78
  Bond restraints: 12516
  Sorted by residual:
  bond pdb=" CB  ILE A 801 "
       pdb=" CG2 ILE A 801 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.23e+00
  bond pdb=" CB  ILE B 801 "
       pdb=" CG2 ILE B 801 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  bond pdb=" CA  THR A 895 "
       pdb=" CB  THR A 895 "
    ideal  model  delta    sigma   weight residual
    1.527  1.540 -0.013 1.61e-02 3.86e+03 6.12e-01
  bond pdb=" CG  LEU B 843 "
       pdb=" CD2 LEU B 843 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 3.30e-02 9.18e+02 5.84e-01
  bond pdb=" CA  THR B 895 "
       pdb=" CB  THR B 895 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.61e-02 3.86e+03 5.71e-01
  ... (remaining 12511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 16541
        1.21 -     2.42: 263
        2.42 -     3.64: 85
        3.64 -     4.85: 13
        4.85 -     6.06: 9
  Bond angle restraints: 16911
  Sorted by residual:
  angle pdb=" C   GLU B1106 "
        pdb=" CA  GLU B1106 "
        pdb=" CB  GLU B1106 "
      ideal   model   delta    sigma   weight residual
     116.54  110.48    6.06 1.15e+00 7.56e-01 2.78e+01
  angle pdb=" N   ILE A 845 "
        pdb=" CA  ILE A 845 "
        pdb=" C   ILE A 845 "
      ideal   model   delta    sigma   weight residual
     112.96  109.42    3.54 1.00e+00 1.00e+00 1.25e+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  109.42    3.54 1.00e+00 1.00e+00 1.25e+01
  angle pdb=" CA  GLU B1106 "
        pdb=" C   GLU B1106 "
        pdb=" N   PHE B1107 "
      ideal   model   delta    sigma   weight residual
     119.52  117.00    2.52 7.90e-01 1.60e+00 1.02e+01
  angle pdb=" C   SER B 657 "
        pdb=" N   GLU B 658 "
        pdb=" CA  GLU B 658 "
      ideal   model   delta    sigma   weight residual
     121.54  126.50   -4.96 1.91e+00 2.74e-01 6.73e+00
  ... (remaining 16906 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 6968
       15.88 -    31.77: 441
       31.77 -    47.65: 86
       47.65 -    63.53: 13
       63.53 -    79.41: 5
  Dihedral angle restraints: 7513
    sinusoidal: 3102
      harmonic: 4411
  Sorted by residual:
  dihedral pdb=" CA  GLU B1073 "
           pdb=" C   GLU B1073 "
           pdb=" N   LEU B1074 "
           pdb=" CA  LEU B1074 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.49   23.51     0      5.00e+00 4.00e-02 2.21e+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 -157.41  -22.59     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  PRO A 938 "
           pdb=" C   PRO A 938 "
           pdb=" N   LEU A 939 "
           pdb=" CA  LEU A 939 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.09  -21.91     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 7510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1036
       0.026 -    0.053: 467
       0.053 -    0.079: 204
       0.079 -    0.105: 82
       0.105 -    0.132: 38
  Chirality restraints: 1827
  Sorted by residual:
  chirality pdb=" CA  THR B 895 "
            pdb=" N   THR B 895 "
            pdb=" C   THR B 895 "
            pdb=" CB  THR B 895 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CA  THR A 895 "
            pdb=" N   THR A 895 "
            pdb=" C   THR A 895 "
            pdb=" CB  THR A 895 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  VAL A 669 "
            pdb=" N   VAL A 669 "
            pdb=" C   VAL A 669 "
            pdb=" CB  VAL A 669 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1824 not shown)

  Planarity restraints: 2157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 937 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO A 938 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.028 5.00e-02 4.00e+02   4.19e-02 2.81e+00
        pdb=" N   PRO B 938 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 858 "    0.014 2.00e-02 2.50e+03   8.40e-03 1.41e+00
        pdb=" CG  TYR B 858 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 858 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 858 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 858 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 858 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 858 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 858 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2154 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1623
        2.75 -     3.29: 11801
        3.29 -     3.83: 20557
        3.83 -     4.36: 26228
        4.36 -     4.90: 43818
  Nonbonded interactions: 104027
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B1043 "
            pdb=" OE1 GLU B1173 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OH  TYR B 923 "
            pdb=" OD2 ASP B 997 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR A1043 "
            pdb=" OE1 GLU A1173 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ARG A 447 "
            pdb=" OG1 THR A 451 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   PRO A1095 "
            pdb=" OH  TYR A1124 "
     model   vdw
     2.274 3.040
  ... (remaining 104022 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 414 through 1028 or resid 1030 through 1192))
  selection = (chain 'B' and (resid 414 through 1028 or resid 1030 through 1192))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.430
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.220
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:6.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12516  Z= 0.120
  Angle     :  0.458   6.059  16911  Z= 0.253
  Chirality :  0.040   0.132   1827
  Planarity :  0.003   0.046   2157
  Dihedral  : 10.981  79.413   4687
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.70 %
  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:  0.51 (0.22), residues: 1497
  helix:  1.05 (0.20), residues: 659
  sheet: -0.49 (0.40), residues: 182
  loop : -0.01 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 736 
 TYR   0.018   0.001   TYR B 858 
 PHE   0.008   0.001   PHE A 990 
 TRP   0.007   0.001   TRP B 861 
 HIS   0.003   0.001   HIS B1192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12516)
  covalent geometry    : angle       0.45781 (16911)
  hydrogen bonds       : bond        0.23204 (  566)
  hydrogen bonds       : angle       6.18153 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  756 MET cc_start: 0.8055 (tpp) cc_final: 0.7755 (tpt)
REVERT: A  970 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: B  970 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7833 (mt-10)
REVERT: B 1111 GLU cc_start: 0.8266 (pm20) cc_final: 0.8039 (pm20)
  outliers start: 2
  outliers final: 0
  residues processed: 83
  average time/residue: 0.8811
  time to fit residues: 77.8782
Evaluate side-chains
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.0870
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1078 HIS
A1092 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.078520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.057120 restraints weight = 29744.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.2730 rms_B_bonded: 2.92
r_work: 0.2568 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2438 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2442 r_free = 0.2442    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2442 r_free = 0.2442    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12516  Z= 0.148
  Angle     :  0.514   6.469  16911  Z= 0.277
  Chirality :  0.042   0.150   1827
  Planarity :  0.004   0.047   2157
  Dihedral  :  4.220  25.166   1671
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.87 %
    Favored  : 95.53 %
  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:  0.84 (0.22), residues: 1497
  helix:  1.46 (0.20), residues: 689
  sheet: -0.40 (0.39), residues: 192
  loop : -0.05 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 985 
 TYR   0.019   0.001   TYR B 858 
 PHE   0.011   0.001   PHE B 990 
 TRP   0.006   0.001   TRP A 599 
 HIS   0.017   0.001   HIS A1078 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12516)
  covalent geometry    : angle       0.51400 (16911)
  hydrogen bonds       : bond        0.05542 (  566)
  hydrogen bonds       : angle       4.46005 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  970 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8361 (mt-10)
REVERT: B  756 MET cc_start: 0.8539 (tpp) cc_final: 0.8335 (tpp)
REVERT: B  970 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8304 (mt-10)
  outliers start: 8
  outliers final: 2
  residues processed: 67
  average time/residue: 0.8501
  time to fit residues: 61.0030
Evaluate side-chains
  59 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 126 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 138 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1078 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.076798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.054953 restraints weight = 35024.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 3.13
r_work: 0.2536 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2521
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2521 r_free = 0.2521    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2521 r_free = 0.2521    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2521
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12516  Z= 0.207
  Angle     :  0.532   6.081  16911  Z= 0.286
  Chirality :  0.044   0.141   1827
  Planarity :  0.004   0.048   2157
  Dihedral  :  4.460  27.898   1671
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  5.31 %
    Favored  : 93.93 %
  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:  0.72 (0.22), residues: 1497
  helix:  1.47 (0.20), residues: 687
  sheet: -0.52 (0.39), residues: 192
  loop : -0.23 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 985 
 TYR   0.023   0.001   TYR B 858 
 PHE   0.013   0.001   PHE A 990 
 TRP   0.007   0.001   TRP A 861 
 HIS   0.004   0.001   HIS B1078 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (12516)
  covalent geometry    : angle       0.53232 (16911)
  hydrogen bonds       : bond        0.05358 (  566)
  hydrogen bonds       : angle       4.27418 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A  929 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7879 (ptm-80)
REVERT: A  970 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8277 (mt-10)
REVERT: B  926 SER cc_start: 0.8843 (m) cc_final: 0.8583 (p)
REVERT: B  970 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8236 (mt-10)
REVERT: B  983 LEU cc_start: 0.8934 (tm) cc_final: 0.8625 (tp)
  outliers start: 10
  outliers final: 4
  residues processed: 69
  average time/residue: 0.8191
  time to fit residues: 60.7394
Evaluate side-chains
  67 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain B residue  960 ILE
Chi-restraints excluded: chain B residue  988 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 140 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 74 optimal weight:    0.2980
   chunk 131 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 139 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0270
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1078 HIS
B1092 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.079098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.057293 restraints weight = 37476.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 3.22
r_work: 0.2590 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2575 r_free = 0.2575    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2575 r_free = 0.2575    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12516  Z= 0.113
  Angle     :  0.467   5.770  16911  Z= 0.250
  Chirality :  0.041   0.139   1827
  Planarity :  0.003   0.047   2157
  Dihedral  :  4.172  25.978   1671
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.22 %
    Favored  : 93.10 %
  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:  0.85 (0.22), residues: 1497
  helix:  1.65 (0.20), residues: 689
  sheet: -0.48 (0.39), residues: 192
  loop : -0.24 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 985 
 TYR   0.019   0.001   TYR B 858 
 PHE   0.011   0.001   PHE A 990 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.019   0.001   HIS B1078 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (12516)
  covalent geometry    : angle       0.46701 (16911)
  hydrogen bonds       : bond        0.04421 (  566)
  hydrogen bonds       : angle       4.12562 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  756 MET cc_start: 0.8317 (tpp) cc_final: 0.8114 (tpp)
REVERT: A  915 GLN cc_start: 0.8569 (pm20) cc_final: 0.8357 (mm110)
REVERT: A  970 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: B  523 GLN cc_start: 0.8473 (tp40) cc_final: 0.7990 (tp-100)
REVERT: B  658 GLU cc_start: 0.7777 (tp30) cc_final: 0.7443 (tm-30)
REVERT: B  756 MET cc_start: 0.8308 (tpp) cc_final: 0.8087 (tpp)
REVERT: B  926 SER cc_start: 0.8900 (m) cc_final: 0.8584 (p)
REVERT: B  970 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8182 (mt-10)
REVERT: B  983 LEU cc_start: 0.8902 (tm) cc_final: 0.8600 (tp)
  outliers start: 9
  outliers final: 3
  residues processed: 71
  average time/residue: 0.7923
  time to fit residues: 60.4991
Evaluate side-chains
  67 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 MET
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 145 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0060
   chunk 125 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 124 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0070
   chunk 132 optimal weight:    2.9990
   overall best weight:    0.4214

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1078 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.079764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.057725 restraints weight = 44911.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.48
r_work: 0.2595 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12516  Z= 0.105
  Angle     :  0.444   5.406  16911  Z= 0.238
  Chirality :  0.040   0.137   1827
  Planarity :  0.003   0.049   2157
  Dihedral  :  4.011  24.959   1671
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.67 %
    Favored  : 92.65 %
  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:  0.97 (0.22), residues: 1497
  helix:  1.73 (0.20), residues: 693
  sheet: -0.42 (0.39), residues: 192
  loop : -0.18 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 985 
 TYR   0.017   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.013   0.001   HIS B1078 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (12516)
  covalent geometry    : angle       0.44429 (16911)
  hydrogen bonds       : bond        0.04145 (  566)
  hydrogen bonds       : angle       4.01863 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  915 GLN cc_start: 0.8624 (pm20) cc_final: 0.8305 (mm110)
REVERT: A  926 SER cc_start: 0.8953 (m) cc_final: 0.8606 (p)
REVERT: A  970 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8224 (mt-10)
REVERT: B  523 GLN cc_start: 0.8460 (tp40) cc_final: 0.7984 (tp-100)
REVERT: B  658 GLU cc_start: 0.7820 (tp30) cc_final: 0.7458 (tm-30)
REVERT: B  756 MET cc_start: 0.8317 (tpp) cc_final: 0.8050 (tpp)
REVERT: B  926 SER cc_start: 0.8937 (m) cc_final: 0.8597 (p)
REVERT: B  970 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8175 (mt-10)
REVERT: B  983 LEU cc_start: 0.8901 (tm) cc_final: 0.8614 (tp)
  outliers start: 9
  outliers final: 3
  residues processed: 74
  average time/residue: 0.7243
  time to fit residues: 58.0247
Evaluate side-chains
  70 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 90 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 148 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 142 optimal weight:    0.0010
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1078 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.079486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.057718 restraints weight = 35354.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.17
r_work: 0.2604 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2588 r_free = 0.2588    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2588 r_free = 0.2588    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12516  Z= 0.114
  Angle     :  0.448   5.376  16911  Z= 0.240
  Chirality :  0.041   0.136   1827
  Planarity :  0.003   0.049   2157
  Dihedral  :  4.020  24.852   1671
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.05 %
    Favored  : 91.74 %
  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 (0.22), residues: 1497
  helix:  1.76 (0.20), residues: 693
  sheet: -0.40 (0.40), residues: 192
  loop : -0.18 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 985 
 TYR   0.018   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.007   0.001   TRP A1189 
 HIS   0.005   0.001   HIS B1078 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12516)
  covalent geometry    : angle       0.44767 (16911)
  hydrogen bonds       : bond        0.04166 (  566)
  hydrogen bonds       : angle       3.98547 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  912 ARG cc_start: 0.8966 (ttt-90) cc_final: 0.8715 (ttm-80)
REVERT: A  915 GLN cc_start: 0.8611 (pm20) cc_final: 0.8298 (mm110)
REVERT: A  926 SER cc_start: 0.8959 (m) cc_final: 0.8663 (p)
REVERT: A  970 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: B  523 GLN cc_start: 0.8457 (tp40) cc_final: 0.7978 (tp-100)
REVERT: B  658 GLU cc_start: 0.7788 (tp30) cc_final: 0.7427 (tm-30)
REVERT: B  926 SER cc_start: 0.8939 (m) cc_final: 0.8600 (p)
REVERT: B  970 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: B  983 LEU cc_start: 0.8905 (tm) cc_final: 0.8616 (tp)
REVERT: B 1112 GLU cc_start: 0.8405 (tt0) cc_final: 0.8156 (pt0)
  outliers start: 16
  outliers final: 7
  residues processed: 79
  average time/residue: 0.7626
  time to fit residues: 64.6552
Evaluate side-chains
  76 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  586 MET
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 55 optimal weight:    0.0980
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 139 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 79 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.078017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.056281 restraints weight = 32788.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 3.07
r_work: 0.2574 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12516  Z= 0.148
  Angle     :  0.472   5.515  16911  Z= 0.253
  Chirality :  0.042   0.136   1827
  Planarity :  0.004   0.050   2157
  Dihedral  :  4.187  25.669   1671
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  7.73 %
    Favored  : 91.51 %
  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:  0.92 (0.22), residues: 1497
  helix:  1.69 (0.20), residues: 693
  sheet: -0.47 (0.39), residues: 192
  loop : -0.20 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 985 
 TYR   0.020   0.001   TYR B 858 
 PHE   0.013   0.001   PHE A 990 
 TRP   0.006   0.001   TRP B 820 
 HIS   0.003   0.001   HIS B1192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12516)
  covalent geometry    : angle       0.47222 (16911)
  hydrogen bonds       : bond        0.04496 (  566)
  hydrogen bonds       : angle       4.02437 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A  926 SER cc_start: 0.8967 (m) cc_final: 0.8652 (p)
REVERT: A  970 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: B  658 GLU cc_start: 0.7859 (tp30) cc_final: 0.7508 (tm-30)
REVERT: B  926 SER cc_start: 0.8942 (m) cc_final: 0.8614 (p)
REVERT: B  970 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8177 (mt-10)
REVERT: B  983 LEU cc_start: 0.8925 (tm) cc_final: 0.8640 (tp)
REVERT: B 1112 GLU cc_start: 0.8412 (tt0) cc_final: 0.8156 (pt0)
  outliers start: 10
  outliers final: 5
  residues processed: 72
  average time/residue: 0.7853
  time to fit residues: 60.9622
Evaluate side-chains
  71 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 108 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 128 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.078382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.057065 restraints weight = 28290.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 2.86
r_work: 0.2596 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2466 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12516  Z= 0.136
  Angle     :  0.466   5.609  16911  Z= 0.250
  Chirality :  0.041   0.137   1827
  Planarity :  0.004   0.048   2157
  Dihedral  :  4.153  25.465   1671
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  7.96 %
    Favored  : 91.13 %
  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:  0.93 (0.22), residues: 1497
  helix:  1.71 (0.20), residues: 693
  sheet: -0.48 (0.39), residues: 192
  loop : -0.20 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 985 
 TYR   0.020   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12516)
  covalent geometry    : angle       0.46622 (16911)
  hydrogen bonds       : bond        0.04381 (  566)
  hydrogen bonds       : angle       4.01195 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  915 GLN cc_start: 0.8698 (pm20) cc_final: 0.8444 (mm110)
REVERT: A  926 SER cc_start: 0.8963 (m) cc_final: 0.8626 (p)
REVERT: A  970 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8363 (mt-10)
REVERT: B  658 GLU cc_start: 0.7966 (tp30) cc_final: 0.7565 (tm-30)
REVERT: B  926 SER cc_start: 0.8948 (m) cc_final: 0.8602 (p)
REVERT: B  970 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8355 (mt-10)
REVERT: B  983 LEU cc_start: 0.8917 (tm) cc_final: 0.8626 (tp)
REVERT: B 1112 GLU cc_start: 0.8476 (tt0) cc_final: 0.8234 (pt0)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.7228
  time to fit residues: 57.0251
Evaluate side-chains
  74 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  586 MET
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 127 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 148 optimal weight:    1.9990
   chunk 133 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.079105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.056924 restraints weight = 42602.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 3.43
r_work: 0.2579 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2562 r_free = 0.2562    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12516  Z= 0.119
  Angle     :  0.451   5.408  16911  Z= 0.242
  Chirality :  0.041   0.136   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  4.056  24.834   1671
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.26 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.22), residues: 1497
  helix:  1.75 (0.20), residues: 693
  sheet: -0.46 (0.39), residues: 192
  loop : -0.18 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 985 
 TYR   0.018   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS B1192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (12516)
  covalent geometry    : angle       0.45067 (16911)
  hydrogen bonds       : bond        0.04184 (  566)
  hydrogen bonds       : angle       3.97627 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A  915 GLN cc_start: 0.8640 (pm20) cc_final: 0.8393 (mm110)
REVERT: A  926 SER cc_start: 0.8961 (m) cc_final: 0.8634 (p)
REVERT: A  970 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: B  523 GLN cc_start: 0.8449 (tp40) cc_final: 0.7957 (tp-100)
REVERT: B  658 GLU cc_start: 0.7866 (tp30) cc_final: 0.7504 (tm-30)
REVERT: B  926 SER cc_start: 0.8945 (m) cc_final: 0.8611 (p)
REVERT: B  970 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8218 (mt-10)
REVERT: B  983 LEU cc_start: 0.8896 (tm) cc_final: 0.8615 (tp)
REVERT: B 1112 GLU cc_start: 0.8413 (tt0) cc_final: 0.8166 (pt0)
  outliers start: 9
  outliers final: 8
  residues processed: 72
  average time/residue: 0.7343
  time to fit residues: 57.2459
Evaluate side-chains
  76 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  586 MET
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 144 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0000
   chunk 134 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.079497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.058516 restraints weight = 37592.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.2795 rms_B_bonded: 3.12
r_work: 0.2632 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12516  Z= 0.116
  Angle     :  0.450   5.345  16911  Z= 0.241
  Chirality :  0.041   0.138   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  4.038  24.659   1671
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.34 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.22), residues: 1497
  helix:  1.76 (0.20), residues: 693
  sheet: -0.47 (0.39), residues: 192
  loop : -0.21 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 985 
 TYR   0.018   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS B1192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12516)
  covalent geometry    : angle       0.44966 (16911)
  hydrogen bonds       : bond        0.04153 (  566)
  hydrogen bonds       : angle       3.95631 ( 1590)

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

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

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2994 Ramachandran restraints generated.
    1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A  915 GLN cc_start: 0.8622 (pm20) cc_final: 0.8382 (mm110)
REVERT: A  926 SER cc_start: 0.8995 (m) cc_final: 0.8714 (p)
REVERT: A  970 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8209 (mt-10)
REVERT: B  523 GLN cc_start: 0.8446 (tp40) cc_final: 0.7952 (tp-100)
REVERT: B  658 GLU cc_start: 0.7798 (tp30) cc_final: 0.7468 (tm-30)
REVERT: B  926 SER cc_start: 0.8987 (m) cc_final: 0.8688 (p)
REVERT: B  970 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: B  983 LEU cc_start: 0.8916 (tm) cc_final: 0.8636 (tp)
REVERT: B 1112 GLU cc_start: 0.8424 (tt0) cc_final: 0.8176 (pt0)
  outliers start: 8
  outliers final: 8
  residues processed: 73
  average time/residue: 0.7590
  time to fit residues: 60.1257
Evaluate side-chains
  75 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  801 ILE
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  586 MET
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    0.3980
   chunk 139 optimal weight:    0.7980
   chunk 109 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 148 optimal weight:    0.0010
   chunk 136 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 90 optimal weight:    0.3980
   chunk 130 optimal weight:    0.7980
   chunk 132 optimal weight:    0.4980
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 753 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.080396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.059526 restraints weight = 27460.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 2.81
r_work: 0.2655 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12516  Z= 0.099
  Angle     :  0.435   5.832  16911  Z= 0.232
  Chirality :  0.040   0.135   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  3.902  23.836   1671
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.42 %
    Favored  : 90.98 %
  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 (0.22), residues: 1497
  helix:  1.83 (0.20), residues: 693
  sheet: -0.41 (0.39), residues: 192
  loop : -0.18 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 985 
 TYR   0.017   0.001   TYR B 858 
 PHE   0.012   0.001   PHE A 990 
 TRP   0.007   0.001   TRP B1189 
 HIS   0.002   0.000   HIS B 887 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (12516)
  covalent geometry    : angle       0.43549 (16911)
  hydrogen bonds       : bond        0.03901 (  566)
  hydrogen bonds       : angle       3.90963 ( 1590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5206.91 seconds
wall clock time: 89 minutes 22.91 seconds (5362.91 seconds total)