Starting phenix.real_space_refine
on Sat Jan 18 15:12:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygh_39250/01_2025/8ygh_39250.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygh_39250/01_2025/8ygh_39250.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ygh_39250/01_2025/8ygh_39250.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygh_39250/01_2025/8ygh_39250.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygh_39250/01_2025/8ygh_39250.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygh_39250/01_2025/8ygh_39250.cif"
  }
  resolution = 2.77
  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=   0.041
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      52      5.16       5
     C    7856      2.51       5
     N    2104      2.21       5
     O    2232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12244
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 755, 6122
          Classifications: {'peptide': 755}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 724}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 755, 6122
          Classifications: {'peptide': 755}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 724}
          Chain breaks: 1
  Time building chain proxies: 7.79, per 1000 atoms: 0.64
  Number of scatterers: 12244
  At special positions: 0
  Unit cell: (116.64, 110.16, 116.64, 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      52     16.00
     O    2232      8.00
     N    2104      7.00
     C    7856      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: 3.12
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2836

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 16 sheets defined
      51.5% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 439 through 451
    Processing helix  chain 'A' and resid 496 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 548 through 560
    Processing helix  chain 'A' and resid 560 through 565
      removed outlier: 4.074A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL A 565 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 565'
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.815A  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: 3.731A  pdb=" N   HIS A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 635
    Processing helix  chain 'A' and resid 645 through 654
    Processing helix  chain 'A' and resid 657 through 664
      removed outlier: 3.501A  pdb=" N   LEU A 664 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 683
    Processing helix  chain 'A' and resid 686 through 705
      removed outlier: 4.597A  pdb=" N   LYS A 696 " --> pdb=" O   GLN A 692 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 738 through 750
      removed outlier: 3.564A  pdb=" N   PHE A 750 " --> pdb=" O   ALA A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 809 through 814
    Processing helix  chain 'A' and resid 817 through 821
      removed outlier: 3.605A  pdb=" N   TRP A 820 " --> pdb=" O   GLU A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 878
      removed outlier: 4.448A  pdb=" N   LYS A 878 " --> pdb=" O   ALA A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 892
    Processing helix  chain 'A' and resid 942 through 953
      removed outlier: 3.598A  pdb=" N   SER A 953 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 958
    Processing helix  chain 'A' and resid 982 through 990
    Processing helix  chain 'A' and resid 997 through 1004
    Processing helix  chain 'A' and resid 1027 through 1075
      removed outlier: 3.514A  pdb=" N   ILE A1031 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
      removed outlier: 6.030A  pdb=" N   ALA A1072 " --> pdb=" O   ILE A1068 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASP A1073 " --> pdb=" O   ASN A1069 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU A1074 " --> pdb=" O   GLU A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1092
      removed outlier: 3.872A  pdb=" N   GLY A1086 " --> pdb=" O   GLU A1082 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1118
      removed outlier: 4.573A  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 1159
      removed outlier: 4.195A  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 453
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 522 through 528
    Processing helix  chain 'B' and resid 546 through 560
    Processing helix  chain 'B' and resid 560 through 565
      removed outlier: 4.054A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL B 565 " --> pdb=" O   PRO B 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 560 through 565'
    Processing helix  chain 'B' and resid 592 through 603
    Processing helix  chain 'B' and resid 616 through 620
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.973A  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: 3.568A  pdb=" N   LEU B 648 " --> pdb=" O   SER B 644 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE B 653 " --> pdb=" O   PHE B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 665
    Processing helix  chain 'B' and resid 672 through 683
      removed outlier: 3.694A  pdb=" N   VAL B 682 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 705
      removed outlier: 3.979A  pdb=" N   THR B 695 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.700A  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 750
      removed outlier: 3.599A  pdb=" N   PHE B 750 " --> pdb=" O   ALA B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 754 through 767
    Processing helix  chain 'B' and resid 787 through 791
      removed outlier: 3.660A  pdb=" N   LEU B 790 " --> pdb=" O   SER B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 806 through 814
    Processing helix  chain 'B' and resid 815 through 822
      removed outlier: 4.064A  pdb=" N   TRP B 820 " --> pdb=" O   THR B 816 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   LEU B 821 " --> pdb=" O   GLU B 817 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 822 " --> pdb=" O   ASP B 818 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 878
      removed outlier: 4.382A  pdb=" N   LYS B 878 " --> pdb=" O   ALA B 874 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 882 through 892
    Processing helix  chain 'B' and resid 942 through 953
      removed outlier: 3.592A  pdb=" N   SER B 953 " --> pdb=" O   SER B 949 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 953 through 958
    Processing helix  chain 'B' and resid 982 through 990
    Processing helix  chain 'B' and resid 997 through 1004
    Processing helix  chain 'B' and resid 1027 through 1069
      removed outlier: 3.595A  pdb=" N   ILE B1031 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1070 through 1075
    Processing helix  chain 'B' and resid 1084 through 1092
      removed outlier: 3.884A  pdb=" N   ILE B1088 " --> pdb=" O   GLU B1084 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1117
    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 1159
      removed outlier: 3.568A  pdb=" N   LYS B1138 " --> pdb=" O   LEU B1134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1187
      removed outlier: 3.680A  pdb=" N   TRP B1170 " --> pdb=" O   GLY B1166 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469
      removed outlier: 6.066A  pdb=" N   LEU A 434 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   CYS A 537 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ALA A 436 " --> pdb=" O   CYS A 537 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 7.861A  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
    Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.724A  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 912
    Processing sheet with id=AA7, first strand: chain 'A' and resid 923 through 926
      removed outlier: 3.608A  pdb=" N   MET A 931 " --> pdb=" O   SER A 926 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1013 through 1016
      removed outlier: 4.292A  pdb=" N   LEU A1013 " --> pdb=" O   PHE A1025 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 465 through 469
      removed outlier: 6.118A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 639 " --> pdb=" O   VAL B 569 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ILE B 685 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
      removed outlier: 5.922A  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
    Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.813A  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: 5.852A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1013 through 1016
      removed outlier: 4.403A  pdb=" N   LEU B1013 " --> pdb=" O   PHE B1025 " (cutoff:3.500A)

    574 hydrogen bonds defined for protein.
    1623 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: 4.80

  Time building geometry restraints manager: 3.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3949
        1.34 -     1.46: 2597
        1.46 -     1.58: 5904
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 12532
  Sorted by residual:
  bond pdb=" C   ILE A 685 "
       pdb=" N   PRO A 686 "
    ideal  model  delta    sigma   weight residual
    1.331  1.375 -0.044 1.31e-02 5.83e+03 1.15e+01
  bond pdb=" C   ILE B 685 "
       pdb=" N   PRO B 686 "
    ideal  model  delta    sigma   weight residual
    1.332  1.372 -0.040 1.32e-02 5.74e+03 9.39e+00
  bond pdb=" CA  GLU A1112 "
       pdb=" C   GLU A1112 "
    ideal  model  delta    sigma   weight residual
    1.522  1.557 -0.035 1.39e-02 5.18e+03 6.30e+00
  bond pdb=" CA  VAL A 569 "
       pdb=" C   VAL A 569 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.026 1.26e-02 6.30e+03 4.12e+00
  bond pdb=" CA  VAL B 569 "
       pdb=" C   VAL B 569 "
    ideal  model  delta    sigma   weight residual
    1.522  1.500  0.022 1.21e-02 6.83e+03 3.24e+00
  ... (remaining 12527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 16723
        2.47 -     4.95: 162
        4.95 -     7.42: 30
        7.42 -     9.90: 12
        9.90 -    12.37: 5
  Bond angle restraints: 16932
  Sorted by residual:
  angle pdb=" N   SER A 605 "
        pdb=" CA  SER A 605 "
        pdb=" C   SER A 605 "
      ideal   model   delta    sigma   weight residual
     111.28  120.90   -9.62 1.09e+00 8.42e-01 7.79e+01
  angle pdb=" N   LEU A1113 "
        pdb=" CA  LEU A1113 "
        pdb=" C   LEU A1113 "
      ideal   model   delta    sigma   weight residual
     110.97  102.31    8.66 1.09e+00 8.42e-01 6.31e+01
  angle pdb=" N   THR A 604 "
        pdb=" CA  THR A 604 "
        pdb=" C   THR A 604 "
      ideal   model   delta    sigma   weight residual
     111.28  119.68   -8.40 1.09e+00 8.42e-01 5.93e+01
  angle pdb=" N   GLU A1111 "
        pdb=" CA  GLU A1111 "
        pdb=" C   GLU A1111 "
      ideal   model   delta    sigma   weight residual
     110.97  117.68   -6.71 1.09e+00 8.42e-01 3.79e+01
  angle pdb=" C   ILE B 685 "
        pdb=" N   PRO B 686 "
        pdb=" CA  PRO B 686 "
      ideal   model   delta    sigma   weight residual
     119.76  114.27    5.49 1.00e+00 1.00e+00 3.01e+01
  ... (remaining 16927 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 6576
       17.40 -    34.80: 706
       34.80 -    52.20: 184
       52.20 -    69.60: 43
       69.60 -    87.00: 21
  Dihedral angle restraints: 7530
    sinusoidal: 3104
      harmonic: 4426
  Sorted by residual:
  dihedral pdb=" CA  LYS B 893 "
           pdb=" C   LYS B 893 "
           pdb=" N   ILE B 894 "
           pdb=" CA  ILE B 894 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.90   18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  GLN A1157 "
           pdb=" C   GLN A1157 "
           pdb=" N   LEU A1158 "
           pdb=" CA  LEU A1158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.01   16.99     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  THR B1109 "
           pdb=" C   THR B1109 "
           pdb=" N   ILE B1110 "
           pdb=" CA  ILE B1110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.37  -16.63     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1669
       0.072 -    0.144: 153
       0.144 -    0.216: 5
       0.216 -    0.288: 2
       0.288 -    0.361: 1
  Chirality restraints: 1830
  Sorted by residual:
  chirality pdb=" CA  GLU A1111 "
            pdb=" N   GLU A1111 "
            pdb=" C   GLU A1111 "
            pdb=" CB  GLU A1111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  SER A 605 "
            pdb=" N   SER A 605 "
            pdb=" C   SER A 605 "
            pdb=" CB  SER A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  THR A 604 "
            pdb=" N   THR A 604 "
            pdb=" C   THR A 604 "
            pdb=" CB  THR A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1827 not shown)

  Planarity restraints: 2166
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B1095 "   -0.038 5.00e-02 4.00e+02   5.82e-02 5.42e+00
        pdb=" N   PRO B1096 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B1096 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B1096 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B1131 "   -0.140 9.50e-02 1.11e+02   6.33e-02 3.47e+00
        pdb=" NE  ARG B1131 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG B1131 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG B1131 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B1131 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 568 "    0.008 2.00e-02 2.50e+03   1.74e-02 3.01e+00
        pdb=" C   PHE A 568 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE A 568 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 569 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2163 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2213
        2.76 -     3.30: 11943
        3.30 -     3.83: 21327
        3.83 -     4.37: 25391
        4.37 -     4.90: 42639
  Nonbonded interactions: 103513
  Sorted by model distance:
  nonbonded pdb=" O   TYR A1067 "
            pdb=" OG  SER A1071 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   THR B1123 "
            pdb=" OG  SER B1127 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OH  TYR A1043 "
            pdb=" OE1 GLU A1173 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OH  TYR A 614 "
            pdb=" OE2 GLU A 624 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER B 787 "
            pdb=" OD2 ASP B 794 "
     model   vdw
     2.291 3.040
  ... (remaining 103508 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: 0.06
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     31.190
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
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   0.044  12532  Z= 0.180
  Angle     :  0.644  12.373  16932  Z= 0.353
  Chirality :  0.043   0.361   1830
  Planarity :  0.004   0.063   2166
  Dihedral  : 16.161  87.004   4694
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.55 %
    Favored  : 78.71 %
  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:  0.53 (0.23), residues: 1502
  helix:  1.56 (0.21), residues: 656
  sheet: -0.41 (0.41), residues: 178
  loop : -0.61 (0.24), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1189 
 HIS   0.003   0.000   HIS A 690 
 PHE   0.011   0.001   PHE B 629 
 TYR   0.007   0.001   TYR B 520 
 ARG   0.018   0.000   ARG B1131 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 1.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  970 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8844 (mm-30)
REVERT: B  688 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8997 (m)
  outliers start: 23
  outliers final: 15
  residues processed: 91
  average time/residue: 1.3712
  time to fit residues: 136.0261
Evaluate side-chains
  82 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  853 SER
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain B residue  501 ASN
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  688 SER
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  955 ASN
Chi-restraints excluded: chain B residue 1121 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 117 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0980
   chunk 136 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.063178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.044208 restraints weight = 38591.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.2729 rms_B_bonded: 3.45
r_work: 0.2567 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12532  Z= 0.262
  Angle     :  0.542   7.888  16932  Z= 0.285
  Chirality :  0.042   0.170   1830
  Planarity :  0.004   0.047   2166
  Dihedral  :  5.618  68.139   1698
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.05 %
    Favored  : 79.85 %
  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:  0.44 (0.22), residues: 1502
  helix:  1.47 (0.21), residues: 666
  sheet: -0.53 (0.39), residues: 188
  loop : -0.66 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 820 
 HIS   0.005   0.001   HIS B 789 
 PHE   0.011   0.001   PHE B1094 
 TYR   0.011   0.001   TYR B 520 
 ARG   0.004   0.000   ARG A 734 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 67
  time to evaluate  : 1.386 
Fit side-chains
REVERT: A 1066 ARG cc_start: 0.9083 (ttt-90) cc_final: 0.8876 (ttt180)
REVERT: B  688 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8968 (m)
REVERT: B  929 ARG cc_start: 0.9350 (ptm-80) cc_final: 0.8941 (ptm-80)
REVERT: B  957 MET cc_start: 0.9122 (mmm) cc_final: 0.8235 (mpp)
  outliers start: 41
  outliers final: 15
  residues processed: 100
  average time/residue: 1.2133
  time to fit residues: 133.5417
Evaluate side-chains
  74 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  688 SER
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
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 128 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 129 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0050
   chunk 12 optimal weight:    0.0770
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.5152

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN
B 623 HIS
B 887 HIS
B1010 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.064414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.045906 restraints weight = 38806.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 3.41
r_work: 0.2617 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12532  Z= 0.146
  Angle     :  0.510   7.402  16932  Z= 0.264
  Chirality :  0.040   0.150   1830
  Planarity :  0.003   0.042   2166
  Dihedral  :  5.426  70.562   1689
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.95 %
    Favored  : 79.62 %
  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:  0.43 (0.22), residues: 1502
  helix:  1.53 (0.21), residues: 658
  sheet: -0.52 (0.39), residues: 188
  loop : -0.71 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1189 
 HIS   0.003   0.000   HIS B1092 
 PHE   0.008   0.001   PHE B 632 
 TYR   0.009   0.001   TYR B 520 
 ARG   0.010   0.000   ARG B1131 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 1.394 
Fit side-chains
REVERT: A 1066 ARG cc_start: 0.9120 (ttt-90) cc_final: 0.8782 (ttt180)
REVERT: B  524 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8749 (pp20)
REVERT: B  688 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9042 (m)
REVERT: B  957 MET cc_start: 0.9163 (mmm) cc_final: 0.8214 (mpp)
REVERT: B 1066 ARG cc_start: 0.9242 (ttt90) cc_final: 0.8997 (ttt180)
  outliers start: 32
  outliers final: 13
  residues processed: 92
  average time/residue: 1.4046
  time to fit residues: 141.0396
Evaluate side-chains
  80 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  688 SER
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    0.0770
   chunk 89 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 114 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 137 optimal weight:    4.9990
   chunk 113 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.0942

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.063712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.044920 restraints weight = 38478.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2747 rms_B_bonded: 3.41
r_work: 0.2589 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12532  Z= 0.202
  Angle     :  0.529   8.504  16932  Z= 0.272
  Chirality :  0.041   0.146   1830
  Planarity :  0.003   0.039   2166
  Dihedral  :  5.221  69.421   1688
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.94 %
    Favored  : 79.17 %
  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:  0.48 (0.22), residues: 1502
  helix:  1.58 (0.21), residues: 658
  sheet: -0.47 (0.40), residues: 188
  loop : -0.72 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1189 
 HIS   0.004   0.001   HIS B 892 
 PHE   0.007   0.001   PHE B 596 
 TYR   0.011   0.001   TYR B 520 
 ARG   0.005   0.000   ARG B1140 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 1.411 
Fit side-chains
REVERT: A  994 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8225 (pp20)
REVERT: A 1042 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9409 (tm)
REVERT: A 1066 ARG cc_start: 0.9115 (ttt-90) cc_final: 0.8761 (ttt-90)
REVERT: A 1111 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9146 (pm20)
REVERT: B  931 MET cc_start: 0.9061 (ttm) cc_final: 0.8752 (ttt)
REVERT: B  957 MET cc_start: 0.9203 (mmm) cc_final: 0.8301 (mpp)
  outliers start: 25
  outliers final: 15
  residues processed: 94
  average time/residue: 1.4814
  time to fit residues: 151.2121
Evaluate side-chains
  76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 1.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 53 optimal weight:    0.0670
   chunk 110 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0770
   chunk 113 optimal weight:    1.9990
   chunk 138 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 127 optimal weight:    5.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.064098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.045585 restraints weight = 38729.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 3.41
r_work: 0.2611 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12532  Z= 0.165
  Angle     :  0.530   8.662  16932  Z= 0.270
  Chirality :  0.040   0.149   1830
  Planarity :  0.003   0.037   2166
  Dihedral  :  5.186  70.640   1687
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.94 %
    Favored  : 79.09 %
  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:  0.50 (0.22), residues: 1502
  helix:  1.62 (0.21), residues: 658
  sheet: -0.40 (0.40), residues: 188
  loop : -0.74 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1189 
 HIS   0.002   0.000   HIS B 892 
 PHE   0.007   0.001   PHE A 559 
 TYR   0.010   0.001   TYR B 520 
 ARG   0.011   0.000   ARG B1131 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 1.434 
Fit side-chains
REVERT: A  970 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8972 (mm-30)
REVERT: A  994 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8204 (pp20)
REVERT: A 1042 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9382 (tm)
REVERT: A 1066 ARG cc_start: 0.9147 (ttt-90) cc_final: 0.8791 (ttt-90)
REVERT: B  524 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8797 (pp20)
REVERT: B  957 MET cc_start: 0.9210 (mmm) cc_final: 0.8299 (mpp)
REVERT: B 1094 PHE cc_start: 0.8001 (m-80) cc_final: 0.7745 (m-80)
  outliers start: 26
  outliers final: 13
  residues processed: 91
  average time/residue: 1.3922
  time to fit residues: 138.0498
Evaluate side-chains
  79 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0050
   chunk 36 optimal weight:    0.6980
   chunk 148 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0170
   chunk 83 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.5434

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.064695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.045965 restraints weight = 39116.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2780 rms_B_bonded: 3.49
r_work: 0.2624 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  12532  Z= 0.156
  Angle     :  0.532   8.996  16932  Z= 0.270
  Chirality :  0.040   0.151   1830
  Planarity :  0.003   0.036   2166
  Dihedral  :  5.155  72.269   1687
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.23 %
    Favored  : 77.88 %
  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:  0.53 (0.22), residues: 1502
  helix:  1.65 (0.21), residues: 658
  sheet: -0.39 (0.40), residues: 188
  loop : -0.74 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1189 
 HIS   0.002   0.000   HIS B 892 
 PHE   0.008   0.001   PHE A 559 
 TYR   0.010   0.001   TYR B 520 
 ARG   0.008   0.000   ARG B 662 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 1.384 
Fit side-chains
REVERT: A  994 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8178 (pp20)
REVERT: A 1042 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9386 (tm)
REVERT: A 1066 ARG cc_start: 0.9150 (ttt-90) cc_final: 0.8776 (ttt-90)
REVERT: A 1111 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9154 (pm20)
REVERT: B  524 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8837 (pp20)
REVERT: B  957 MET cc_start: 0.9213 (mmm) cc_final: 0.8312 (mpp)
REVERT: B 1094 PHE cc_start: 0.8024 (m-80) cc_final: 0.7177 (m-80)
  outliers start: 25
  outliers final: 13
  residues processed: 90
  average time/residue: 1.3828
  time to fit residues: 135.9639
Evaluate side-chains
  76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 119 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 129 optimal weight:    6.9990
   chunk 127 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN
B 879 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.061915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.043126 restraints weight = 39049.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2700 rms_B_bonded: 3.41
r_work: 0.2533 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12532  Z= 0.331
  Angle     :  0.594   9.586  16932  Z= 0.304
  Chirality :  0.043   0.150   1830
  Planarity :  0.004   0.043   2166
  Dihedral  :  5.271  63.888   1687
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.61 %
    Favored  : 77.35 %
  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:  0.45 (0.22), residues: 1502
  helix:  1.48 (0.21), residues: 674
  sheet: -0.23 (0.42), residues: 176
  loop : -0.78 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 820 
 HIS   0.008   0.001   HIS B 892 
 PHE   0.010   0.001   PHE A 629 
 TYR   0.014   0.001   TYR B 520 
 ARG   0.017   0.001   ARG B1131 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 1.507 
Fit side-chains
REVERT: A  994 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8325 (pp20)
REVERT: A 1042 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9391 (tm)
REVERT: A 1048 MET cc_start: 0.9553 (mmm) cc_final: 0.9305 (mmm)
REVERT: A 1060 MET cc_start: 0.7444 (pp-130) cc_final: 0.7187 (ttp)
REVERT: A 1066 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8848 (ttt180)
REVERT: B  957 MET cc_start: 0.9204 (mmm) cc_final: 0.8460 (mpp)
REVERT: B 1066 ARG cc_start: 0.9113 (ttt90) cc_final: 0.8803 (ttt90)
REVERT: B 1094 PHE cc_start: 0.8041 (m-80) cc_final: 0.7221 (m-80)
REVERT: B 1151 ARG cc_start: 0.9438 (OUTLIER) cc_final: 0.9062 (mmm160)
  outliers start: 27
  outliers final: 14
  residues processed: 90
  average time/residue: 1.3513
  time to fit residues: 132.9629
Evaluate side-chains
  75 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue 1110 ILE
Chi-restraints excluded: chain B residue 1118 LEU
Chi-restraints excluded: chain B residue 1151 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 143 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.062283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.043714 restraints weight = 39103.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 3.41
r_work: 0.2550 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  12532  Z= 0.260
  Angle     :  0.578  10.061  16932  Z= 0.294
  Chirality :  0.042   0.188   1830
  Planarity :  0.004   0.053   2166
  Dihedral  :  5.219  63.862   1687
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.98 %
    Favored  : 77.20 %
  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:  0.44 (0.22), residues: 1502
  helix:  1.44 (0.21), residues: 672
  sheet: -0.25 (0.41), residues: 176
  loop : -0.74 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1189 
 HIS   0.005   0.001   HIS B 892 
 PHE   0.008   0.001   PHE A 629 
 TYR   0.012   0.001   TYR B 520 
 ARG   0.013   0.000   ARG B 662 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 1.227 
Fit side-chains
REVERT: A  994 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8282 (pp20)
REVERT: A 1042 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9354 (tm)
REVERT: A 1048 MET cc_start: 0.9545 (mmm) cc_final: 0.9286 (mmm)
REVERT: A 1066 ARG cc_start: 0.9113 (ttt-90) cc_final: 0.8836 (ttt180)
REVERT: A 1111 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9154 (pm20)
REVERT: A 1131 ARG cc_start: 0.8824 (tpm-80) cc_final: 0.8400 (tpm170)
REVERT: B  524 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8845 (pp20)
REVERT: B  957 MET cc_start: 0.9189 (mmm) cc_final: 0.8363 (mpp)
  outliers start: 24
  outliers final: 14
  residues processed: 87
  average time/residue: 1.4346
  time to fit residues: 135.7412
Evaluate side-chains
  77 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 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 84 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0040
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.063972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.045222 restraints weight = 38846.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 3.46
r_work: 0.2601 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12532  Z= 0.171
  Angle     :  0.566  11.859  16932  Z= 0.285
  Chirality :  0.041   0.189   1830
  Planarity :  0.003   0.063   2166
  Dihedral  :  5.111  69.743   1687
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 21.67 %
    Favored  : 76.89 %
  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:  0.44 (0.22), residues: 1502
  helix:  1.50 (0.21), residues: 666
  sheet: -0.27 (0.41), residues: 176
  loop : -0.77 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1189 
 HIS   0.005   0.001   HIS B 892 
 PHE   0.008   0.001   PHE A 559 
 TYR   0.011   0.001   TYR A1043 
 ARG   0.012   0.000   ARG B 662 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 1.629 
Fit side-chains
REVERT: A  987 MET cc_start: 0.9482 (mmm) cc_final: 0.9256 (mmm)
REVERT: A  994 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8242 (pp20)
REVERT: A 1042 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9326 (tm)
REVERT: A 1048 MET cc_start: 0.9548 (mmm) cc_final: 0.9290 (mmm)
REVERT: A 1066 ARG cc_start: 0.9141 (ttt-90) cc_final: 0.8785 (ttt-90)
REVERT: A 1111 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.9151 (pm20)
REVERT: A 1131 ARG cc_start: 0.8834 (tpm-80) cc_final: 0.8409 (tpm170)
REVERT: B  524 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8873 (pp20)
REVERT: B  931 MET cc_start: 0.9180 (ttp) cc_final: 0.8978 (ptm)
REVERT: B  957 MET cc_start: 0.9203 (mmm) cc_final: 0.8363 (mpp)
REVERT: B 1066 ARG cc_start: 0.9087 (ttt90) cc_final: 0.8777 (ptt90)
REVERT: B 1094 PHE cc_start: 0.7967 (m-80) cc_final: 0.7141 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 84
  average time/residue: 1.3950
  time to fit residues: 128.1588
Evaluate side-chains
  76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:   30.0000
   chunk 84 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0670
   overall best weight:    1.5722

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

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 = 0.062489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.043896 restraints weight = 38809.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 3.41
r_work: 0.2556 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  12532  Z= 0.261
  Angle     :  0.599  11.058  16932  Z= 0.302
  Chirality :  0.042   0.176   1830
  Planarity :  0.004   0.049   2166
  Dihedral  :  5.100  66.870   1687
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 22.05 %
    Favored  : 76.82 %
  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:  0.42 (0.22), residues: 1502
  helix:  1.45 (0.21), residues: 666
  sheet: -0.28 (0.41), residues: 176
  loop : -0.75 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B 789 
 PHE   0.008   0.001   PHE B 596 
 TYR   0.013   0.001   TYR B 520 
 ARG   0.011   0.000   ARG B 662 

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

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

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3004 Ramachandran restraints generated.
    1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 1.759 
Fit side-chains
REVERT: A  994 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8282 (pp20)
REVERT: A 1042 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9336 (tm)
REVERT: A 1048 MET cc_start: 0.9556 (mmm) cc_final: 0.9303 (mmm)
REVERT: A 1066 ARG cc_start: 0.9133 (ttt-90) cc_final: 0.8853 (ttt180)
REVERT: A 1111 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9146 (pm20)
REVERT: A 1131 ARG cc_start: 0.8885 (tpm-80) cc_final: 0.8461 (tpm170)
REVERT: B  524 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8857 (pp20)
REVERT: B  929 ARG cc_start: 0.9263 (pmm-80) cc_final: 0.9020 (pmm-80)
REVERT: B  957 MET cc_start: 0.9197 (mmm) cc_final: 0.8389 (mpp)
REVERT: B 1094 PHE cc_start: 0.8030 (m-80) cc_final: 0.7145 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 78
  average time/residue: 1.3955
  time to fit residues: 119.2058
Evaluate side-chains
  76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1111 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain B residue  524 GLU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 THR
Chi-restraints excluded: chain B residue  797 SER
Chi-restraints excluded: chain B residue  825 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    0.0670
   chunk 82 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 148 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.9522

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

Flipped N/Q/H residues before XYZ refinement:
A 915 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.063332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.044796 restraints weight = 38730.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 3.41
r_work: 0.2589 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12532  Z= 0.197
  Angle     :  0.590  13.175  16932  Z= 0.296
  Chirality :  0.042   0.215   1830
  Planarity :  0.003   0.040   2166
  Dihedral  :  5.032  68.812   1686
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 22.05 %
    Favored  : 76.82 %
  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:  0.43 (0.22), residues: 1502
  helix:  1.47 (0.21), residues: 666
  sheet: -0.30 (0.41), residues: 176
  loop : -0.75 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B 892 
 PHE   0.007   0.001   PHE A 559 
 TYR   0.010   0.001   TYR B 520 
 ARG   0.010   0.000   ARG B 662 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6948.91 seconds
wall clock time: 124 minutes 12.07 seconds (7452.07 seconds total)