Starting phenix.real_space_refine
on Wed May 14 22:39:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j89_36064/05_2025/8j89_36064.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j89_36064/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j89_36064/05_2025/8j89_36064.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j89_36064/05_2025/8j89_36064.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j89_36064/05_2025/8j89_36064.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j89_36064/05_2025/8j89_36064.cif"
  }
  resolution = 2.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.21, per 1000 atoms: 0.84
  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: 2.71
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  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: 1.58
  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: 4.61

  Time building geometry restraints manager: 3.21 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:             7.010
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     33.840
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.820
-------------------------------------------------------------------------------
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 (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:  0.51 (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
 TRP   0.007   0.001   TRP B 861 
 HIS   0.003   0.001   HIS B1192 
 PHE   0.008   0.001   PHE A 990 
 TYR   0.018   0.001   TYR B 858 
 ARG   0.002   0.000   ARG A 736 

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

*********************** 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  : 1.526 
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: 1.7533
  time to fit residues: 155.7765
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  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    3.9990
   chunk 113 optimal weight:    0.5980
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3145 r_free = 0.3145 target = 0.078449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.057543 restraints weight = 24772.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2739 rms_B_bonded: 2.68
r_work: 0.2584 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2454 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2458
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2458 r_free = 0.2458    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2458 r_free = 0.2458    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2458
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1125

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= 0.149
  Angle     :  0.513   6.429  16911  Z= 0.276
  Chirality :  0.042   0.149   1827
  Planarity :  0.004   0.047   2157
  Dihedral  :  4.238  25.444   1671
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.94 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.22), residues: 1497
  helix:  1.43 (0.20), residues: 689
  sheet: -0.40 (0.39), residues: 192
  loop : -0.06 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 599 
 HIS   0.018   0.001   HIS A1078 
 PHE   0.011   0.001   PHE B 990 
 TYR   0.019   0.001   TYR B 858 
 ARG   0.008   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05581 (  566)
  hydrogen bonds       : angle       4.44468 ( 1590)
  covalent geometry    : bond        0.00339 (12516)
  covalent geometry    : angle       0.51277 (16911)

*********************** 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
  72 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.520 
Fit side-chains
REVERT: A  970 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: B  756 MET cc_start: 0.8523 (tpp) cc_final: 0.8313 (tpp)
REVERT: B  970 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8281 (mt-10)
  outliers start: 8
  outliers final: 2
  residues processed: 68
  average time/residue: 1.6834
  time to fit residues: 123.5529
Evaluate side-chains
  60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.0770
   chunk 35 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 119 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 145 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A1078 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.079069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.057885 restraints weight = 28171.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 2.84
r_work: 0.2591 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2461 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12516  Z= 0.127
  Angle     :  0.475   5.953  16911  Z= 0.255
  Chirality :  0.041   0.142   1827
  Planarity :  0.004   0.047   2157
  Dihedral  :  4.135  25.709   1671
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  5.69 %
    Favored  : 93.78 %
  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 (0.22), residues: 1497
  helix:  1.61 (0.20), residues: 687
  sheet: -0.44 (0.39), residues: 192
  loop : -0.16 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1078 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.019   0.001   TYR B 858 
 ARG   0.008   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04752 (  566)
  hydrogen bonds       : angle       4.18287 ( 1590)
  covalent geometry    : bond        0.00286 (12516)
  covalent geometry    : angle       0.47463 (16911)

*********************** 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
  77 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 1.300 
Fit side-chains
REVERT: A  756 MET cc_start: 0.8443 (tpp) cc_final: 0.8181 (tpp)
REVERT: A  915 GLN cc_start: 0.8683 (pm20) cc_final: 0.8380 (mm110)
REVERT: A  929 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7833 (ptm-80)
REVERT: A  931 ILE cc_start: 0.8550 (mm) cc_final: 0.8263 (mm)
REVERT: A  970 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8342 (mt-10)
REVERT: A  983 LEU cc_start: 0.8901 (tm) cc_final: 0.8585 (tp)
REVERT: B  658 GLU cc_start: 0.7902 (tp30) cc_final: 0.7497 (tm-30)
REVERT: B  926 SER cc_start: 0.8853 (m) cc_final: 0.8571 (p)
REVERT: B  970 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8309 (mt-10)
  outliers start: 7
  outliers final: 2
  residues processed: 72
  average time/residue: 1.5209
  time to fit residues: 118.5981
Evaluate side-chains
  66 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain B residue  960 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    0.7980
   chunk 109 optimal weight:    0.0970
   chunk 8 optimal weight:    0.7980
   chunk 114 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 105 optimal weight:    0.1980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
B1078 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.079669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.057902 restraints weight = 37355.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 3.23
r_work: 0.2605 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1496

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     :  0.456   5.481  16911  Z= 0.244
  Chirality :  0.041   0.138   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  4.058  25.172   1671
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.07 %
    Favored  : 93.25 %
  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 (0.22), residues: 1497
  helix:  1.72 (0.20), residues: 685
  sheet: -0.39 (0.40), residues: 192
  loop : -0.19 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.021   0.001   HIS B1078 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.018   0.001   TYR B 858 
 ARG   0.008   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04321 (  566)
  hydrogen bonds       : angle       4.08087 ( 1590)
  covalent geometry    : bond        0.00249 (12516)
  covalent geometry    : angle       0.45576 (16911)

*********************** 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
  77 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.310 
Fit side-chains
REVERT: A  756 MET cc_start: 0.8260 (tpp) cc_final: 0.8017 (tpp)
REVERT: A  915 GLN cc_start: 0.8603 (pm20) cc_final: 0.8299 (mm110)
REVERT: A  970 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8175 (mt-10)
REVERT: B  523 GLN cc_start: 0.8470 (tp40) cc_final: 0.7996 (tp-100)
REVERT: B  658 GLU cc_start: 0.7763 (tp30) cc_final: 0.7412 (tm-30)
REVERT: B  926 SER cc_start: 0.8916 (m) cc_final: 0.8599 (p)
REVERT: B  970 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8178 (mt-10)
  outliers start: 9
  outliers final: 2
  residues processed: 70
  average time/residue: 1.5468
  time to fit residues: 117.0279
Evaluate side-chains
  63 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 90 optimal weight:    0.4980
   chunk 84 optimal weight:    4.9990
   chunk 146 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 96 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3111 r_free = 0.3111 target = 0.076467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.054530 restraints weight = 36863.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2675 rms_B_bonded: 3.19
r_work: 0.2501 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2510 r_free = 0.2510    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 = 0.2510 r_free = 0.2510    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12516  Z= 0.218
  Angle     :  0.523   6.158  16911  Z= 0.280
  Chirality :  0.044   0.140   1827
  Planarity :  0.004   0.048   2157
  Dihedral  :  4.437  27.506   1671
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.67 %
    Favored  : 92.42 %
  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:  0.77 (0.22), residues: 1497
  helix:  1.56 (0.20), residues: 691
  sheet: -0.55 (0.39), residues: 192
  loop : -0.27 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 861 
 HIS   0.014   0.001   HIS B1078 
 PHE   0.014   0.001   PHE A 990 
 TYR   0.024   0.001   TYR B 858 
 ARG   0.007   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05082 (  566)
  hydrogen bonds       : angle       4.15742 ( 1590)
  covalent geometry    : bond        0.00523 (12516)
  covalent geometry    : angle       0.52262 (16911)

*********************** 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
  77 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.413 
Fit side-chains
REVERT: A  756 MET cc_start: 0.8333 (tpp) cc_final: 0.8080 (tpp)
REVERT: A  926 SER cc_start: 0.8931 (m) cc_final: 0.8622 (p)
REVERT: A  929 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8398 (ptm-80)
REVERT: B  658 GLU cc_start: 0.7916 (tp30) cc_final: 0.7559 (tm-30)
REVERT: B  846 MET cc_start: 0.9238 (mtp) cc_final: 0.8988 (mtp)
REVERT: B  926 SER cc_start: 0.8921 (m) cc_final: 0.8599 (p)
REVERT: B  970 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8222 (mt-10)
REVERT: B  983 LEU cc_start: 0.8915 (tm) cc_final: 0.8616 (tp)
  outliers start: 12
  outliers final: 4
  residues processed: 70
  average time/residue: 1.5519
  time to fit residues: 118.2851
Evaluate side-chains
  68 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  929 ARG
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  960 ILE
Chi-restraints excluded: chain B residue  988 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 129 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0570
   chunk 20 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 112 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0370
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.4176

-------------------------------------------------------------------------------
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 = 0.3168 r_free = 0.3168 target = 0.079602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.057889 restraints weight = 37316.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 3.22
r_work: 0.2606 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
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 = 0.45   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: 0.8619
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12516  Z= 0.105
  Angle     :  0.450   5.614  16911  Z= 0.240
  Chirality :  0.040   0.137   1827
  Planarity :  0.003   0.047   2157
  Dihedral  :  4.066  25.104   1671
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  7.35 %
    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 (0.22), residues: 1497
  helix:  1.71 (0.20), residues: 693
  sheet: -0.47 (0.39), residues: 192
  loop : -0.18 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 820 
 HIS   0.004   0.001   HIS A1078 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.019   0.001   TYR B 858 
 ARG   0.008   0.000   ARG B 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04149 (  566)
  hydrogen bonds       : angle       4.02882 ( 1590)
  covalent geometry    : bond        0.00229 (12516)
  covalent geometry    : angle       0.45005 (16911)

*********************** 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
  74 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.435 
Fit side-chains
REVERT: A  926 SER cc_start: 0.8949 (m) cc_final: 0.8649 (p)
REVERT: A  970 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8209 (mt-10)
REVERT: B  523 GLN cc_start: 0.8456 (tp40) cc_final: 0.7975 (tp-100)
REVERT: B  658 GLU cc_start: 0.7789 (tp30) cc_final: 0.7459 (tm-30)
REVERT: B  926 SER cc_start: 0.8927 (m) cc_final: 0.8601 (p)
REVERT: B  970 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8149 (mt-10)
REVERT: B  983 LEU cc_start: 0.8898 (tm) cc_final: 0.8603 (tp)
  outliers start: 8
  outliers final: 5
  residues processed: 70
  average time/residue: 1.4356
  time to fit residues: 109.5211
Evaluate side-chains
  68 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
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 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 47 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0000
   chunk 130 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 131 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0670
   chunk 10 optimal weight:    0.0020
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.2730

-------------------------------------------------------------------------------
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 = 0.3219 r_free = 0.3219 target = 0.081724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.060211 restraints weight = 43910.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 3.45
r_work: 0.2631 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12516  Z= 0.092
  Angle     :  0.424   5.128  16911  Z= 0.227
  Chirality :  0.040   0.136   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  3.838  23.821   1671
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.88 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.22), residues: 1497
  helix:  1.84 (0.20), residues: 693
  sheet: -0.37 (0.40), residues: 192
  loop : -0.16 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1189 
 HIS   0.004   0.000   HIS A1078 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.016   0.001   TYR B 858 
 ARG   0.009   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  566)
  hydrogen bonds       : angle       3.93104 ( 1590)
  covalent geometry    : bond        0.00190 (12516)
  covalent geometry    : angle       0.42439 (16911)

*********************** 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
  82 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 1.461 
Fit side-chains
REVERT: A  926 SER cc_start: 0.8976 (m) cc_final: 0.8668 (p)
REVERT: A  970 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8185 (mt-10)
REVERT: B  523 GLN cc_start: 0.8428 (tp40) cc_final: 0.7946 (tp-100)
REVERT: B  658 GLU cc_start: 0.7785 (tp30) cc_final: 0.7421 (tm-30)
REVERT: B  926 SER cc_start: 0.8940 (m) cc_final: 0.8602 (p)
REVERT: B  948 GLU cc_start: 0.8646 (mm-30) cc_final: 0.7978 (mt-10)
REVERT: B  970 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: B  983 LEU cc_start: 0.8886 (tm) cc_final: 0.8595 (tp)
  outliers start: 9
  outliers final: 3
  residues processed: 79
  average time/residue: 1.4117
  time to fit residues: 121.4155
Evaluate side-chains
  69 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0980
   chunk 134 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 76 optimal weight:    0.0980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3179 r_free = 0.3179 target = 0.080216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.059220 restraints weight = 28225.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 2.84
r_work: 0.2647 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2518 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2499 r_free = 0.2499    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2499 r_free = 0.2499    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1744

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     :  0.437   5.593  16911  Z= 0.233
  Chirality :  0.040   0.135   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  3.904  23.947   1671
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.64 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.22), residues: 1497
  helix:  1.83 (0.20), residues: 693
  sheet: -0.34 (0.40), residues: 192
  loop : -0.15 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A1078 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.016   0.001   TYR B 858 
 ARG   0.008   0.000   ARG B 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03954 (  566)
  hydrogen bonds       : angle       3.92041 ( 1590)
  covalent geometry    : bond        0.00231 (12516)
  covalent geometry    : angle       0.43684 (16911)

*********************** 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
  77 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A  926 SER cc_start: 0.8982 (m) cc_final: 0.8659 (p)
REVERT: A  970 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8276 (mt-10)
REVERT: B  523 GLN cc_start: 0.8468 (tp40) cc_final: 0.7989 (tp-100)
REVERT: B  658 GLU cc_start: 0.7901 (tp30) cc_final: 0.7495 (tm-30)
REVERT: B  926 SER cc_start: 0.8960 (m) cc_final: 0.8620 (p)
REVERT: B  948 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8063 (mt-10)
REVERT: B  970 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8254 (mt-10)
REVERT: B  983 LEU cc_start: 0.8882 (tm) cc_final: 0.8602 (tp)
  outliers start: 9
  outliers final: 6
  residues processed: 72
  average time/residue: 1.4434
  time to fit residues: 112.9320
Evaluate side-chains
  71 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
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  931 ILE
Chi-restraints excluded: chain A residue  960 ILE
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain B residue  701 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0980
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0980
   chunk 129 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.5382

-------------------------------------------------------------------------------
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 = 0.3172 r_free = 0.3172 target = 0.079863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.057927 restraints weight = 37052.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 3.24
r_work: 0.2607 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2590
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2590 r_free = 0.2590    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 = 0.2590 r_free = 0.2590    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12516  Z= 0.112
  Angle     :  0.441   5.247  16911  Z= 0.235
  Chirality :  0.040   0.135   1827
  Planarity :  0.003   0.049   2157
  Dihedral  :  3.945  24.056   1671
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  8.95 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.22), residues: 1497
  helix:  1.81 (0.20), residues: 693
  sheet: -0.36 (0.40), residues: 192
  loop : -0.15 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A1078 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.018   0.001   TYR B 858 
 ARG   0.009   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04054 (  566)
  hydrogen bonds       : angle       3.92561 ( 1590)
  covalent geometry    : bond        0.00252 (12516)
  covalent geometry    : angle       0.44088 (16911)

*********************** 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
  72 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 1.480 
Fit side-chains
REVERT: A  926 SER cc_start: 0.8978 (m) cc_final: 0.8688 (p)
REVERT: A  970 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8173 (mt-10)
REVERT: B  523 GLN cc_start: 0.8424 (tp40) cc_final: 0.7932 (tp-100)
REVERT: B  658 GLU cc_start: 0.7816 (tp30) cc_final: 0.7435 (tm-30)
REVERT: B  926 SER cc_start: 0.8970 (m) cc_final: 0.8663 (p)
REVERT: B  970 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: B  983 LEU cc_start: 0.8873 (tm) cc_final: 0.8597 (tp)
  outliers start: 7
  outliers final: 5
  residues processed: 68
  average time/residue: 1.5034
  time to fit residues: 111.5352
Evaluate side-chains
  69 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 137 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0670
   chunk 126 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 103 optimal weight:    0.3980
   chunk 90 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0870
   overall best weight:    0.4296

-------------------------------------------------------------------------------
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 = 0.3181 r_free = 0.3181 target = 0.080390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.058956 restraints weight = 30868.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 2.99
r_work: 0.2637 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
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   0.027  12516  Z= 0.102
  Angle     :  0.434   5.349  16911  Z= 0.231
  Chirality :  0.040   0.135   1827
  Planarity :  0.003   0.048   2157
  Dihedral  :  3.900  23.543   1671
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  9.25 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.22), residues: 1497
  helix:  1.84 (0.20), residues: 693
  sheet: -0.35 (0.40), residues: 192
  loop : -0.14 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A1078 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.017   0.001   TYR B 858 
 ARG   0.009   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (  566)
  hydrogen bonds       : angle       3.90720 ( 1590)
  covalent geometry    : bond        0.00223 (12516)
  covalent geometry    : angle       0.43359 (16911)

********************** 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
  70 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 1.419 
Fit side-chains
REVERT: A  912 ARG cc_start: 0.8921 (ttt-90) cc_final: 0.8569 (ttm-80)
REVERT: A  926 SER cc_start: 0.9004 (m) cc_final: 0.8707 (p)
REVERT: A  970 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8108 (mt-10)
REVERT: B  523 GLN cc_start: 0.8420 (tp40) cc_final: 0.7927 (tp-100)
REVERT: B  658 GLU cc_start: 0.7810 (tp30) cc_final: 0.7438 (tm-30)
REVERT: B  926 SER cc_start: 0.9007 (m) cc_final: 0.8731 (p)
REVERT: B  970 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: B  983 LEU cc_start: 0.8864 (tm) cc_final: 0.8590 (tp)
  outliers start: 4
  outliers final: 4
  residues processed: 68
  average time/residue: 1.4940
  time to fit residues: 110.2029
Evaluate side-chains
  70 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 143 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 133 optimal weight:    0.5980
   chunk 134 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3145 r_free = 0.3145 target = 0.078410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.056792 restraints weight = 30449.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 2.96
r_work: 0.2587 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    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 = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12516  Z= 0.144
  Angle     :  0.467   5.357  16911  Z= 0.250
  Chirality :  0.041   0.136   1827
  Planarity :  0.004   0.049   2157
  Dihedral  :  4.115  24.909   1671
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  8.95 %
    Favored  : 90.52 %
  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 (0.22), residues: 1497
  helix:  1.74 (0.20), residues: 693
  sheet: -0.43 (0.39), residues: 192
  loop : -0.17 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 820 
 HIS   0.004   0.001   HIS A1078 
 PHE   0.012   0.001   PHE A 990 
 TYR   0.020   0.001   TYR B 858 
 ARG   0.010   0.000   ARG A 985 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04399 (  566)
  hydrogen bonds       : angle       3.97382 ( 1590)
  covalent geometry    : bond        0.00336 (12516)
  covalent geometry    : angle       0.46656 (16911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9452.23 seconds
wall clock time: 164 minutes 15.83 seconds (9855.83 seconds total)