Starting phenix.real_space_refine
on Fri Mar 15 17:38:08 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8b_36066/03_2024/8j8b_36066.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8b_36066/03_2024/8j8b_36066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8b_36066/03_2024/8j8b_36066.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8b_36066/03_2024/8j8b_36066.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8b_36066/03_2024/8j8b_36066.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8b_36066/03_2024/8j8b_36066.pdb"
  }
  resolution = 2.43
  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    7922      2.51       5
     N    2116      2.21       5
     O    2242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  539": "OD1" <-> "OD2"
    Residue "A GLU  948": "OE1" <-> "OE2"
    Residue "A GLU 1041": "OE1" <-> "OE2"
    Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1107": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1111": "OE1" <-> "OE2"
    Residue "B ASP  539": "OD1" <-> "OD2"
    Residue "B GLU  948": "OE1" <-> "OE2"
    Residue "B GLU 1041": "OE1" <-> "OE2"
    Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE 1107": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU 1111": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 12330
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 759, 6165
          Classifications: {'peptide': 759}
          Link IDs: {'PTRANS': 30, 'TRANS': 728}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 759, 6165
          Classifications: {'peptide': 759}
          Link IDs: {'PTRANS': 30, 'TRANS': 728}
          Chain breaks: 1
  Time building chain proxies: 6.36, per 1000 atoms: 0.52
  Number of scatterers: 12330
  At special positions: 0
  Unit cell: (108.73, 107.07, 112.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    2242      8.00
     N    2116      7.00
     C    7922      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 4.46
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2852

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 16 sheets defined
      50.2% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 428 through 431
    Processing helix  chain 'A' and resid 439 through 451
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 497 through 501
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 547 through 560
    Processing helix  chain 'A' and resid 560 through 566
      removed outlier: 3.942A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.603A  pdb=" N   LYS A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.587A  pdb=" N   HIS A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 642 through 653
      removed outlier: 3.818A  pdb=" N   LYS A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLU A 647 " --> pdb=" O   ASP A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 664
      removed outlier: 3.962A  pdb=" N   LYS A 661 " --> pdb=" O   SER A 657 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ARG A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLU A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 683
      removed outlier: 3.718A  pdb=" N   VAL A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 705
      removed outlier: 3.513A  pdb=" N   THR A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   LYS A 696 " --> pdb=" O   GLN A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 738 through 749
    Processing helix  chain 'A' and resid 754 through 765
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.686A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 847
      removed outlier: 3.619A  pdb=" N   GLU A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 877
    Processing helix  chain 'A' and resid 882 through 893
      removed outlier: 4.085A  pdb=" N   LYS A 891 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A 892 " --> pdb=" O   TYR A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 952
    Processing helix  chain 'A' and resid 953 through 958
    Processing helix  chain 'A' and resid 982 through 991
      removed outlier: 4.196A  pdb=" N   VAL A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLU A 988 " --> pdb=" O   ASN A 984 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU A 989 " --> pdb=" O   ARG A 985 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS A 991 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1027 through 1070
      removed outlier: 3.729A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1081 through 1091
      removed outlier: 3.768A  pdb=" N   ILE A1088 " --> pdb=" O   GLU A1084 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A1089 " --> pdb=" O   ALA A1085 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU A1091 " --> pdb=" O   ARG A1087 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.526A  pdb=" N   LEU A1118 " --> pdb=" O   ASN A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1133
    Processing helix  chain 'A' and resid 1134 through 1160
      removed outlier: 3.575A  pdb=" N   ARG A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1187
    Processing helix  chain 'B' and resid 428 through 431
    Processing helix  chain 'B' and resid 439 through 451
    Processing helix  chain 'B' and resid 452 through 456
    Processing helix  chain 'B' and resid 497 through 501
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 522 through 527
    Processing helix  chain 'B' and resid 547 through 560
    Processing helix  chain 'B' and resid 560 through 566
      removed outlier: 3.942A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 602
      removed outlier: 3.603A  pdb=" N   LYS B 602 " --> pdb=" O   ALA B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.586A  pdb=" N   HIS B 631 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 642 through 653
      removed outlier: 3.818A  pdb=" N   LYS B 646 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLU B 647 " --> pdb=" O   ASP B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 664
      removed outlier: 3.961A  pdb=" N   LYS B 661 " --> pdb=" O   SER B 657 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ARG B 662 " --> pdb=" O   GLU B 658 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   GLU B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 683
      removed outlier: 3.719A  pdb=" N   VAL B 682 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 705
      removed outlier: 3.514A  pdb=" N   THR B 695 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   LYS B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 738 through 749
    Processing helix  chain 'B' and resid 754 through 765
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 3.687A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 847
      removed outlier: 3.618A  pdb=" N   GLU B 847 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 877
    Processing helix  chain 'B' and resid 882 through 893
      removed outlier: 4.084A  pdb=" N   LYS B 891 " --> pdb=" O   HIS B 887 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS B 892 " --> pdb=" O   TYR B 888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 942 through 952
    Processing helix  chain 'B' and resid 953 through 958
    Processing helix  chain 'B' and resid 982 through 991
      removed outlier: 4.196A  pdb=" N   VAL B 987 " --> pdb=" O   LEU B 983 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   GLU B 988 " --> pdb=" O   ASN B 984 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU B 989 " --> pdb=" O   ARG B 985 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS B 991 " --> pdb=" O   VAL B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1070
      removed outlier: 3.729A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1081 through 1091
      removed outlier: 3.767A  pdb=" N   ILE B1088 " --> pdb=" O   GLU B1084 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU B1089 " --> pdb=" O   ALA B1085 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU B1091 " --> pdb=" O   ARG B1087 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1119
      removed outlier: 3.525A  pdb=" N   LEU B1118 " --> pdb=" O   ASN B1114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1129 through 1133
    Processing helix  chain 'B' and resid 1134 through 1160
      removed outlier: 3.575A  pdb=" N   ARG B1140 " --> pdb=" O   ALA B1136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419
      removed outlier: 6.182A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE A 685 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   THR A 638 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737
      removed outlier: 3.546A  pdb=" N   ILE A 782 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.544A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 850
    Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913
    Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 926
      removed outlier: 5.846A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A 962 " --> pdb=" O   LYS A 977 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1014 through 1016
    Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419
      removed outlier: 6.183A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   THR B 638 " --> pdb=" O   ILE B 685 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737
      removed outlier: 3.545A  pdb=" N   ILE B 782 " --> pdb=" O   SER B 802 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.544A  pdb=" N   VAL B 825 " --> pdb=" O   ALA B 832 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 850
    Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913
    Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 926
      removed outlier: 5.847A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU B 962 " --> pdb=" O   LYS B 977 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016

    558 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.02

  Time building geometry restraints manager: 4.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3984
        1.34 -     1.46: 2820
        1.46 -     1.58: 5740
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 12622
  Sorted by residual:
  bond pdb=" CB  ASP A 414 "
       pdb=" CG  ASP A 414 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.00e+00
  bond pdb=" CB  ASP B 414 "
       pdb=" CG  ASP B 414 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.00e+00
  bond pdb=" CG  ARG A 734 "
       pdb=" CD  ARG A 734 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.74e-01
  bond pdb=" C   SER A1162 "
       pdb=" N   PRO A1163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 2.34e-02 1.83e+03 5.71e-01
  bond pdb=" CG  ARG B 734 "
       pdb=" CD  ARG B 734 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.62e-01
  ... (remaining 12617 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   106.65: 334
      106.65 -   113.48: 6763
      113.48 -   120.31: 4493
      120.31 -   127.14: 5323
      127.14 -   133.97: 141
  Bond angle restraints: 17054
  Sorted by residual:
  angle pdb=" C   GLY A 472 "
        pdb=" N   VAL A 473 "
        pdb=" CA  VAL A 473 "
      ideal   model   delta    sigma   weight residual
     121.97  126.27   -4.30 1.80e+00 3.09e-01 5.70e+00
  angle pdb=" C   GLY B 472 "
        pdb=" N   VAL B 473 "
        pdb=" CA  VAL B 473 "
      ideal   model   delta    sigma   weight residual
     121.97  126.22   -4.25 1.80e+00 3.09e-01 5.58e+00
  angle pdb=" CA  TYR B1122 "
        pdb=" CB  TYR B1122 "
        pdb=" CG  TYR B1122 "
      ideal   model   delta    sigma   weight residual
     113.90  109.92    3.98 1.80e+00 3.09e-01 4.89e+00
  angle pdb=" CA  TYR A1122 "
        pdb=" CB  TYR A1122 "
        pdb=" CG  TYR A1122 "
      ideal   model   delta    sigma   weight residual
     113.90  109.97    3.93 1.80e+00 3.09e-01 4.77e+00
  angle pdb=" N   PHE B1191 "
        pdb=" CA  PHE B1191 "
        pdb=" CB  PHE B1191 "
      ideal   model   delta    sigma   weight residual
     113.65  110.66    2.99 1.47e+00 4.63e-01 4.15e+00
  ... (remaining 17049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.89: 6827
       11.89 -    23.78: 534
       23.78 -    35.67: 175
       35.67 -    47.57: 34
       47.57 -    59.46: 8
  Dihedral angle restraints: 7578
    sinusoidal: 3128
      harmonic: 4450
  Sorted by residual:
  dihedral pdb=" CA  TYR A1122 "
           pdb=" C   TYR A1122 "
           pdb=" N   THR A1123 "
           pdb=" CA  THR A1123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  TYR B1122 "
           pdb=" C   TYR B1122 "
           pdb=" N   THR B1123 "
           pdb=" CA  THR B1123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  PRO B 938 "
           pdb=" C   PRO B 938 "
           pdb=" N   LEU B 939 "
           pdb=" CA  LEU B 939 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.63  -17.37     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 7575 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1294
       0.034 -    0.068: 414
       0.068 -    0.102: 92
       0.102 -    0.135: 46
       0.135 -    0.169: 2
  Chirality restraints: 1848
  Sorted by residual:
  chirality pdb=" CB  VAL B 473 "
            pdb=" CA  VAL B 473 "
            pdb=" CG1 VAL B 473 "
            pdb=" CG2 VAL B 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CB  VAL A 473 "
            pdb=" CA  VAL A 473 "
            pdb=" CG1 VAL A 473 "
            pdb=" CG2 VAL A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.10e-01
  chirality pdb=" CA  ILE B 685 "
            pdb=" N   ILE B 685 "
            pdb=" C   ILE B 685 "
            pdb=" CB  ILE B 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1845 not shown)

  Planarity restraints: 2176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 937 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A 938 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 938 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 938 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 937 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO B 938 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 938 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 938 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1122 "   -0.020 2.00e-02 2.50e+03   1.10e-02 2.41e+00
        pdb=" CG  TYR A1122 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1122 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1122 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1122 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1122 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1122 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A1122 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2173 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1329
        2.75 -     3.29: 12051
        3.29 -     3.82: 20379
        3.82 -     4.36: 25542
        4.36 -     4.90: 43217
  Nonbonded interactions: 102518
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 712 "
            pdb=" NH1 ARG A 719 "
     model   vdw
     2.210 2.520
  nonbonded pdb=" OD2 ASP B 712 "
            pdb=" NH1 ARG B 719 "
     model   vdw
     2.210 2.520
  nonbonded pdb=" OG  SER B 919 "
            pdb=" OD1 ASN B1007 "
     model   vdw
     2.216 2.440
  nonbonded pdb=" OG  SER A 919 "
            pdb=" OD1 ASN A1007 "
     model   vdw
     2.217 2.440
  nonbonded pdb=" OG  SER B 787 "
            pdb=" OD2 ASP B 794 "
     model   vdw
     2.244 2.440
  ... (remaining 102513 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  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:          13.460
  Check model and map are aligned:         0.200
  Set scattering table:                    0.120
  Process input model:                     32.790
  Find NCS groups from input model:        0.660
  Set up NCS constraints:                  0.070
  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:11.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12622  Z= 0.138
  Angle     :  0.415   4.914  17054  Z= 0.227
  Chirality :  0.038   0.169   1848
  Planarity :  0.003   0.041   2176
  Dihedral  :  9.831  59.457   4726
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.04 (0.22), residues: 1510
  helix:  1.30 (0.20), residues: 658
  sheet:  0.23 (0.40), residues: 198
  loop :  0.38 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 820 
 HIS   0.004   0.001   HIS B1078 
 PHE   0.007   0.001   PHE B 990 
 TYR   0.022   0.001   TYR A1122 
 ARG   0.010   0.000   ARG A 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 MET cc_start: 0.8665 (ptp) cc_final: 0.8372 (ptp)
REVERT: B  701 ASP cc_start: 0.8147 (t70) cc_final: 0.7762 (t70)
REVERT: B  888 TYR cc_start: 0.8843 (t80) cc_final: 0.8640 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 106
  average time/residue: 1.5309
  time to fit residues: 175.1767
Evaluate side-chains
  74 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 113 optimal weight:    0.0980
   chunk 63 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 117 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 136 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12622  Z= 0.232
  Angle     :  0.497   7.486  17054  Z= 0.271
  Chirality :  0.042   0.146   1848
  Planarity :  0.004   0.043   2176
  Dihedral  :  3.959  20.574   1684
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.88 %
    Favored  : 94.44 %
  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:  0.86 (0.22), residues: 1510
  helix:  1.25 (0.21), residues: 690
  sheet:  0.31 (0.43), residues: 168
  loop :  0.03 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 856 
 HIS   0.002   0.001   HIS A 887 
 PHE   0.010   0.001   PHE B 649 
 TYR   0.026   0.001   TYR B1122 
 ARG   0.010   0.001   ARG A 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.595 
Fit side-chains
   revert: symmetry clash
REVERT: A  701 ASP cc_start: 0.8314 (t70) cc_final: 0.8054 (t70)
REVERT: A 1048 MET cc_start: 0.8398 (mtm) cc_final: 0.8196 (mtp)
REVERT: B  662 ARG cc_start: 0.7869 (mpp80) cc_final: 0.7409 (mpp80)
REVERT: B  701 ASP cc_start: 0.8205 (t70) cc_final: 0.7918 (t70)
REVERT: B 1140 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7765 (mtm-85)
  outliers start: 9
  outliers final: 3
  residues processed: 91
  average time/residue: 1.3361
  time to fit residues: 132.4232
Evaluate side-chains
  71 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue 1110 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 135 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12622  Z= 0.223
  Angle     :  0.495  14.803  17054  Z= 0.258
  Chirality :  0.041   0.136   1848
  Planarity :  0.004   0.047   2176
  Dihedral  :  4.083  21.676   1684
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.88 %
    Favored  : 91.44 %
  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: 1510
  helix:  1.35 (0.21), residues: 686
  sheet: -0.34 (0.39), residues: 190
  loop : -0.03 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B1012 
 PHE   0.010   0.001   PHE A 990 
 TYR   0.018   0.001   TYR A1122 
 ARG   0.009   0.000   ARG B 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.8940 (ptt) cc_final: 0.8669 (ptp)
REVERT: A  701 ASP cc_start: 0.8245 (t70) cc_final: 0.8012 (t70)
REVERT: A  924 ASP cc_start: 0.8165 (m-30) cc_final: 0.7912 (m-30)
REVERT: A 1048 MET cc_start: 0.8443 (mtm) cc_final: 0.8157 (mtp)
REVERT: A 1087 ARG cc_start: 0.7923 (ptm-80) cc_final: 0.7559 (mtm-85)
REVERT: B  635 MET cc_start: 0.8922 (ptt) cc_final: 0.8691 (ptp)
REVERT: B  662 ARG cc_start: 0.7970 (mpp80) cc_final: 0.7680 (mpp80)
REVERT: B  701 ASP cc_start: 0.8185 (t70) cc_final: 0.7939 (t70)
REVERT: B  924 ASP cc_start: 0.8162 (m-30) cc_final: 0.7927 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 78
  average time/residue: 1.4638
  time to fit residues: 123.9046
Evaluate side-chains
  70 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  501 ASN
Chi-restraints excluded: chain B residue 1110 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0030
   chunk 65 optimal weight:    0.0570
   chunk 91 optimal weight:    0.0980
   chunk 136 optimal weight:    0.9990
   chunk 144 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 129 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.2708

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12622  Z= 0.128
  Angle     :  0.459  13.481  17054  Z= 0.238
  Chirality :  0.039   0.131   1848
  Planarity :  0.003   0.042   2176
  Dihedral  :  3.856  20.644   1684
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.86 %
    Favored  : 90.54 %
  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:  0.92 (0.22), residues: 1510
  helix:  1.48 (0.21), residues: 688
  sheet: -0.29 (0.39), residues: 190
  loop :  0.05 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 820 
 HIS   0.002   0.000   HIS B1051 
 PHE   0.009   0.001   PHE A 990 
 TYR   0.028   0.001   TYR B1122 
 ARG   0.008   0.000   ARG A 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.8874 (ptt) cc_final: 0.8645 (ptp)
REVERT: A  924 ASP cc_start: 0.8110 (m-30) cc_final: 0.7827 (m-30)
REVERT: A  988 GLU cc_start: 0.8444 (pt0) cc_final: 0.8122 (pp20)
REVERT: A 1087 ARG cc_start: 0.7951 (ptm-80) cc_final: 0.7511 (mtm-85)
REVERT: B  635 MET cc_start: 0.8871 (ptt) cc_final: 0.8671 (ptp)
REVERT: B  701 ASP cc_start: 0.8183 (t70) cc_final: 0.7958 (t70)
REVERT: B  924 ASP cc_start: 0.8102 (m-30) cc_final: 0.7741 (m-30)
REVERT: B 1048 MET cc_start: 0.8393 (mtm) cc_final: 0.8185 (mtp)
  outliers start: 8
  outliers final: 0
  residues processed: 91
  average time/residue: 1.5385
  time to fit residues: 151.4132
Evaluate side-chains
  74 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  12622  Z= 0.368
  Angle     :  0.553  10.902  17054  Z= 0.292
  Chirality :  0.044   0.162   1848
  Planarity :  0.005   0.074   2176
  Dihedral  :  4.426  24.589   1684
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.38 %
    Favored  : 89.71 %
  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:  0.69 (0.22), residues: 1510
  helix:  1.30 (0.21), residues: 690
  sheet: -0.48 (0.39), residues: 190
  loop : -0.06 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 861 
 HIS   0.004   0.001   HIS A1012 
 PHE   0.013   0.002   PHE A 990 
 TYR   0.023   0.001   TYR A1122 
 ARG   0.011   0.001   ARG B 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.8958 (ptt) cc_final: 0.8666 (ptp)
REVERT: A  662 ARG cc_start: 0.8127 (mpt-90) cc_final: 0.7917 (mpp80)
REVERT: A  924 ASP cc_start: 0.8131 (m-30) cc_final: 0.7882 (m-30)
REVERT: A  988 GLU cc_start: 0.8490 (pt0) cc_final: 0.8209 (pp20)
REVERT: A 1087 ARG cc_start: 0.7913 (ptm-80) cc_final: 0.7533 (mtm-85)
REVERT: B  635 MET cc_start: 0.8937 (ptt) cc_final: 0.8708 (ptp)
REVERT: B  701 ASP cc_start: 0.8244 (t70) cc_final: 0.7999 (t70)
REVERT: B  924 ASP cc_start: 0.8136 (m-30) cc_final: 0.7747 (m-30)
REVERT: B  929 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8205 (mtm-85)
REVERT: B 1048 MET cc_start: 0.8433 (mtm) cc_final: 0.8164 (mtp)
REVERT: B 1140 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7913 (mtm-85)
  outliers start: 12
  outliers final: 4
  residues processed: 81
  average time/residue: 1.4430
  time to fit residues: 127.1137
Evaluate side-chains
  70 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 1.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain B residue  803 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 130 optimal weight:    0.0670
   chunk 28 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 35 optimal weight:    0.2980
   chunk 145 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 139 optimal weight:    0.3980
   overall best weight:    0.4918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12622  Z= 0.161
  Angle     :  0.475  12.592  17054  Z= 0.247
  Chirality :  0.040   0.177   1848
  Planarity :  0.003   0.045   2176
  Dihedral  :  4.091  22.658   1684
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.68 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.80 (0.23), residues: 1510
  helix:  1.42 (0.21), residues: 694
  sheet: -0.41 (0.39), residues: 190
  loop : -0.05 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 820 
 HIS   0.002   0.000   HIS A1051 
 PHE   0.008   0.001   PHE A 990 
 TYR   0.027   0.001   TYR A1122 
 ARG   0.013   0.000   ARG B 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.8871 (ptt) cc_final: 0.8662 (ptp)
REVERT: A  924 ASP cc_start: 0.8092 (m-30) cc_final: 0.7856 (m-30)
REVERT: A  988 GLU cc_start: 0.8424 (pt0) cc_final: 0.8184 (pp20)
REVERT: A 1087 ARG cc_start: 0.7883 (ptm-80) cc_final: 0.7490 (mtm-85)
REVERT: B  924 ASP cc_start: 0.8100 (m-30) cc_final: 0.7850 (m-30)
REVERT: B  988 GLU cc_start: 0.8461 (pt0) cc_final: 0.8219 (pp20)
REVERT: B 1048 MET cc_start: 0.8394 (mtm) cc_final: 0.8167 (mtp)
  outliers start: 12
  outliers final: 4
  residues processed: 86
  average time/residue: 1.4159
  time to fit residues: 132.2430
Evaluate side-chains
  77 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ASP
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain B residue  642 ASP
Chi-restraints excluded: chain B residue 1110 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 105 optimal weight:    0.5980
   chunk 122 optimal weight:    0.0670
   chunk 81 optimal weight:    4.9990
   chunk 144 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
A 510 GLN
A1099 HIS
B 510 GLN
B1099 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12622  Z= 0.198
  Angle     :  0.484  12.132  17054  Z= 0.252
  Chirality :  0.041   0.195   1848
  Planarity :  0.004   0.046   2176
  Dihedral  :  4.085  22.625   1684
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.06 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.23), residues: 1510
  helix:  1.46 (0.21), residues: 694
  sheet: -0.50 (0.39), residues: 190
  loop : -0.06 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.011   0.001   PHE A 990 
 TYR   0.029   0.001   TYR B1122 
 ARG   0.014   0.000   ARG A 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 1.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  924 ASP cc_start: 0.8095 (m-30) cc_final: 0.7850 (m-30)
REVERT: A  988 GLU cc_start: 0.8429 (pt0) cc_final: 0.8205 (pp20)
REVERT: A 1087 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7530 (mtm-85)
REVERT: B  924 ASP cc_start: 0.8122 (m-30) cc_final: 0.7746 (m-30)
REVERT: B  988 GLU cc_start: 0.8451 (pt0) cc_final: 0.8228 (pp20)
REVERT: B 1048 MET cc_start: 0.8387 (mtm) cc_final: 0.8166 (mtp)
  outliers start: 10
  outliers final: 4
  residues processed: 83
  average time/residue: 1.5095
  time to fit residues: 135.5219
Evaluate side-chains
  75 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ASP
Chi-restraints excluded: chain B residue  642 ASP
Chi-restraints excluded: chain B residue 1110 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0270
   chunk 91 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0670
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 126 optimal weight:    0.5980
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12622  Z= 0.155
  Angle     :  0.474  12.917  17054  Z= 0.246
  Chirality :  0.040   0.172   1848
  Planarity :  0.003   0.046   2176
  Dihedral  :  3.966  21.921   1684
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.98 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.23), residues: 1510
  helix:  1.53 (0.21), residues: 692
  sheet: -0.44 (0.39), residues: 190
  loop : -0.03 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 820 
 HIS   0.002   0.000   HIS B1099 
 PHE   0.009   0.001   PHE A 990 
 TYR   0.029   0.001   TYR B1122 
 ARG   0.014   0.000   ARG A 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 1.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  924 ASP cc_start: 0.8059 (m-30) cc_final: 0.7697 (m-30)
REVERT: A  988 GLU cc_start: 0.8417 (pt0) cc_final: 0.8212 (pp20)
REVERT: A 1087 ARG cc_start: 0.7882 (ptm-80) cc_final: 0.7560 (mtm-85)
REVERT: B  924 ASP cc_start: 0.8075 (m-30) cc_final: 0.7711 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 82
  average time/residue: 1.3990
  time to fit residues: 125.2854
Evaluate side-chains
  78 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ASP
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain B residue  642 ASP
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 138 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 121 optimal weight:    0.1980
   chunk 127 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 142 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12622  Z= 0.199
  Angle     :  0.489  11.445  17054  Z= 0.256
  Chirality :  0.041   0.175   1848
  Planarity :  0.004   0.050   2176
  Dihedral  :  4.041  22.278   1684
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.98 %
    Favored  : 89.04 %
  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:  0.87 (0.23), residues: 1510
  helix:  1.53 (0.21), residues: 692
  sheet: -0.48 (0.39), residues: 190
  loop : -0.03 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1189 
 HIS   0.002   0.001   HIS A1051 
 PHE   0.011   0.001   PHE B 990 
 TYR   0.031   0.001   TYR A1122 
 ARG   0.016   0.001   ARG A 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  924 ASP cc_start: 0.8066 (m-30) cc_final: 0.7697 (m-30)
REVERT: A  988 GLU cc_start: 0.8417 (pt0) cc_final: 0.8217 (pp20)
REVERT: A 1087 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7547 (mtm-85)
REVERT: B  662 ARG cc_start: 0.7958 (mpp80) cc_final: 0.7244 (mpp80)
REVERT: B  924 ASP cc_start: 0.8111 (m-30) cc_final: 0.7742 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 79
  average time/residue: 1.2478
  time to fit residues: 108.0899
Evaluate side-chains
  78 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ASP
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain B residue  642 ASP
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue 1110 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 149 optimal weight:    0.9980
   chunk 137 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0370
   chunk 94 optimal weight:    1.9990
   chunk 126 optimal weight:    0.3980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12622  Z= 0.183
  Angle     :  0.489  11.391  17054  Z= 0.255
  Chirality :  0.041   0.179   1848
  Planarity :  0.004   0.055   2176
  Dihedral  :  4.019  22.124   1684
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.14 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.23), residues: 1510
  helix:  1.54 (0.21), residues: 692
  sheet: -0.47 (0.39), residues: 190
  loop : -0.03 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B1099 
 PHE   0.010   0.001   PHE B 990 
 TYR   0.031   0.001   TYR A1122 
 ARG   0.015   0.000   ARG B 734 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  924 ASP cc_start: 0.8064 (m-30) cc_final: 0.7698 (m-30)
REVERT: A 1087 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7542 (mtm-85)
REVERT: B  662 ARG cc_start: 0.7950 (mpp80) cc_final: 0.7236 (mpp80)
REVERT: B  924 ASP cc_start: 0.8112 (m-30) cc_final: 0.7735 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 79
  average time/residue: 1.3612
  time to fit residues: 117.6798
Evaluate side-chains
  77 residues out of total 1332 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ASP
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain B residue  642 ASP
Chi-restraints excluded: chain B residue  701 ASP
Chi-restraints excluded: chain B residue  803 VAL
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A1099 HIS
B1099 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.085087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.060720 restraints weight = 22187.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.71
r_work: 0.2634 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2503 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12622  Z= 0.213
  Angle     :  0.503  11.064  17054  Z= 0.262
  Chirality :  0.041   0.180   1848
  Planarity :  0.004   0.056   2176
  Dihedral  :  4.088  22.483   1684
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.14 %
    Favored  : 89.11 %
  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:  0.86 (0.23), residues: 1510
  helix:  1.49 (0.21), residues: 696
  sheet: -0.50 (0.39), residues: 190
  loop : -0.02 (0.26), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B1189 
 HIS   0.002   0.001   HIS A1099 
 PHE   0.010   0.001   PHE B 990 
 TYR   0.031   0.001   TYR B1122 
 ARG   0.015   0.001   ARG A 734 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3564.17 seconds
wall clock time: 64 minutes 47.56 seconds (3887.56 seconds total)