Starting phenix.real_space_refine
on Wed Jul 30 09:48:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9y_36119/07_2025/8j9y_36119.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9y_36119/07_2025/8j9y_36119.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9y_36119/07_2025/8j9y_36119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9y_36119/07_2025/8j9y_36119.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9y_36119/07_2025/8j9y_36119.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9y_36119/07_2025/8j9y_36119.cif"
  }
  resolution = 3.16
  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=   0.045
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    7818      2.51       5
     N    2086      2.21       5
     O    2200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12154
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 6077
          Classifications: {'peptide': 747}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 12.93, per 1000 atoms: 1.06
  Number of scatterers: 12154
  At special positions: 0
  Unit cell: (114.95, 109.25, 111.15, 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    2200      8.00
     N    2086      7.00
     C    7818      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.90
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2812

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 16 sheets defined
      53.7% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.10
  Creating SS restraints...
    Processing helix  chain 'B' and resid 428 through 432
    Processing helix  chain 'B' and resid 439 through 451
    Processing helix  chain 'B' and resid 503 through 513
    Processing helix  chain 'B' and resid 522 through 527
    Processing helix  chain 'B' and resid 541 through 546
    Processing helix  chain 'B' and resid 547 through 560
    Processing helix  chain 'B' and resid 560 through 567
      removed outlier: 3.879A  pdb=" N   ILE B 564 " --> pdb=" O   TRP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 602
      removed outlier: 3.721A  pdb=" N   LYS B 602 " --> pdb=" O   ALA B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 620
      removed outlier: 3.705A  pdb=" N   HIS B 620 " --> pdb=" O   LEU B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 631
      removed outlier: 3.541A  pdb=" N   HIS B 631 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 635
    Processing helix  chain 'B' and resid 642 through 654
      removed outlier: 4.062A  pdb=" N   LYS B 646 " --> pdb=" O   ASP B 642 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLU B 647 " --> pdb=" O   ASP B 643 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 664
    Processing helix  chain 'B' and resid 672 through 683
    Processing helix  chain 'B' and resid 687 through 707
      removed outlier: 3.748A  pdb=" N   THR B 695 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LYS B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLN B 706 " --> pdb=" O   ALA B 702 " (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 766
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 3.951A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 877
    Processing helix  chain 'B' and resid 882 through 893
    Processing helix  chain 'B' and resid 942 through 953
      removed outlier: 3.586A  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 1075
      removed outlier: 3.571A  pdb=" N   ILE B1031 " --> pdb=" O   THR B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
      removed outlier: 3.513A  pdb=" N   LEU B1042 " --> pdb=" O   TYR B1038 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR B1043 " --> pdb=" O   ARG B1039 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLN B1044 " --> pdb=" O   ARG B1040 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS B1045 " --> pdb=" O   GLU B1041 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   ALA B1072 " --> pdb=" O   ILE B1068 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   GLU B1073 " --> pdb=" O   ASN B1069 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1076 through 1079
    Processing helix  chain 'B' and resid 1081 through 1092
    Processing helix  chain 'B' and resid 1098 through 1104
    Processing helix  chain 'B' and resid 1109 through 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 1160
    Processing helix  chain 'B' and resid 1166 through 1187
    Processing helix  chain 'A' and resid 428 through 432
    Processing helix  chain 'A' and resid 439 through 451
    Processing helix  chain 'A' and resid 503 through 513
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 547 through 560
    Processing helix  chain 'A' and resid 560 through 567
      removed outlier: 3.878A  pdb=" N   ILE A 564 " --> pdb=" O   TRP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 3.721A  pdb=" N   LYS A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
      removed outlier: 3.705A  pdb=" N   HIS A 620 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 631
      removed outlier: 3.540A  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 642 through 654
      removed outlier: 4.062A  pdb=" N   LYS A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLU A 647 " --> pdb=" O   ASP A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 664
    Processing helix  chain 'A' and resid 672 through 683
    Processing helix  chain 'A' and resid 687 through 707
      removed outlier: 3.748A  pdb=" N   THR A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LYS A 696 " --> pdb=" O   GLN A 692 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLN A 706 " --> pdb=" O   ALA A 702 " (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 766
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 3.950A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 877
    Processing helix  chain 'A' and resid 882 through 893
    Processing helix  chain 'A' and resid 942 through 953
      removed outlier: 3.585A  pdb=" N   SER A 953 " --> pdb=" O   SER A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 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: 3.570A  pdb=" N   ILE A1031 " --> pdb=" O   THR A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
      removed outlier: 3.512A  pdb=" N   LEU A1042 " --> pdb=" O   TYR A1038 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A1043 " --> pdb=" O   ARG A1039 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLN A1044 " --> pdb=" O   ARG A1040 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A1045 " --> pdb=" O   GLU A1041 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   ALA A1072 " --> pdb=" O   ILE A1068 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   GLU A1073 " --> pdb=" O   ASN A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1079
    Processing helix  chain 'A' and resid 1081 through 1092
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1117
    Processing helix  chain 'A' and resid 1122 through 1127
    Processing helix  chain 'A' and resid 1129 through 1133
    Processing helix  chain 'A' and resid 1134 through 1160
    Processing helix  chain 'A' and resid 1166 through 1187
    Processing sheet with id=AA1, first strand: chain 'B' and resid 418 through 419
      removed outlier: 6.358A  pdb=" N   LEU B 434 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   CYS B 537 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA B 436 " --> pdb=" O   CYS B 537 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE B 534 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LEU B 572 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 572 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   VAL B 569 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590
    Processing sheet with id=AA3, first strand: chain 'B' and resid 736 through 737
    Processing sheet with id=AA4, first strand: chain 'B' and resid 824 through 827
      removed outlier: 4.181A  pdb=" N   VAL B 825 " --> pdb=" O   ALA B 832 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 849 through 852
    Processing sheet with id=AA6, first strand: chain 'B' and resid 910 through 913
    Processing sheet with id=AA7, first strand: chain 'B' and resid 922 through 926
      removed outlier: 6.250A  pdb=" N   THR B 922 " --> pdb=" O   THR B 935 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU B 975 " --> pdb=" O   ILE B 963 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ILE B 963 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LYS B 977 " --> pdb=" O   GLU B 961 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1013 through 1016
      removed outlier: 4.320A  pdb=" N   LEU B1013 " --> pdb=" O   PHE B1025 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 418 through 419
      removed outlier: 6.358A  pdb=" N   LEU A 434 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   CYS A 537 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ALA A 436 " --> pdb=" O   CYS A 537 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE A 534 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   LEU A 572 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   VAL A 569 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590
    Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 737
    Processing sheet with id=AB3, first strand: chain 'A' and resid 824 through 827
      removed outlier: 4.181A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 832 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 852
    Processing sheet with id=AB5, first strand: chain 'A' and resid 910 through 913
    Processing sheet with id=AB6, first strand: chain 'A' and resid 922 through 926
      removed outlier: 6.251A  pdb=" N   THR A 922 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU A 975 " --> pdb=" O   ILE A 963 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ILE A 963 " --> pdb=" O   LEU A 975 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LYS A 977 " --> pdb=" O   GLU A 961 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1016
      removed outlier: 4.321A  pdb=" N   LEU A1013 " --> pdb=" O   PHE A1025 " (cutoff:3.500A)

    598 hydrogen bonds defined for protein.
    1704 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: 4.15

  Time building geometry restraints manager: 3.42 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: 3910
        1.34 -     1.46: 2690
        1.46 -     1.58: 5768
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 12446
  Sorted by residual:
  bond pdb=" CB  PRO A 881 "
       pdb=" CG  PRO A 881 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.68e+00
  bond pdb=" CB  PRO B 881 "
       pdb=" CG  PRO B 881 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.68e+00
  bond pdb=" C   ILE B 896 "
       pdb=" N   LEU B 897 "
    ideal  model  delta    sigma   weight residual
    1.331  1.354 -0.023 2.07e-02 2.33e+03 1.20e+00
  bond pdb=" C   ILE A 896 "
       pdb=" N   LEU A 897 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.022 2.07e-02 2.33e+03 1.17e+00
  bond pdb=" N   LYS A 882 "
       pdb=" CA  LYS A 882 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.29e-02 6.01e+03 8.52e-01
  ... (remaining 12441 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 16502
        1.45 -     2.90: 246
        2.90 -     4.34: 54
        4.34 -     5.79: 10
        5.79 -     7.24: 4
  Bond angle restraints: 16816
  Sorted by residual:
  angle pdb=" N   ASN B 930 "
        pdb=" CA  ASN B 930 "
        pdb=" C   ASN B 930 "
      ideal   model   delta    sigma   weight residual
     111.02  107.36    3.66 1.25e+00 6.40e-01 8.59e+00
  angle pdb=" N   ASN A 930 "
        pdb=" CA  ASN A 930 "
        pdb=" C   ASN A 930 "
      ideal   model   delta    sigma   weight residual
     111.02  107.39    3.63 1.25e+00 6.40e-01 8.41e+00
  angle pdb=" C   HIS A 631 "
        pdb=" N   PHE A 632 "
        pdb=" CA  PHE A 632 "
      ideal   model   delta    sigma   weight residual
     120.82  124.91   -4.09 1.50e+00 4.44e-01 7.42e+00
  angle pdb=" C   SER A 455 "
        pdb=" N   ASN A 456 "
        pdb=" CA  ASN A 456 "
      ideal   model   delta    sigma   weight residual
     121.80  126.86   -5.06 2.44e+00 1.68e-01 4.31e+00
  angle pdb=" CA  LEU A 452 "
        pdb=" CB  LEU A 452 "
        pdb=" CG  LEU A 452 "
      ideal   model   delta    sigma   weight residual
     116.30  123.54   -7.24 3.50e+00 8.16e-02 4.28e+00
  ... (remaining 16811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 6496
       16.96 -    33.91: 738
       33.91 -    50.87: 210
       50.87 -    67.82: 24
       67.82 -    84.78: 6
  Dihedral angle restraints: 7474
    sinusoidal: 3088
      harmonic: 4386
  Sorted by residual:
  dihedral pdb=" CG  ARG A 873 "
           pdb=" CD  ARG A 873 "
           pdb=" NE  ARG A 873 "
           pdb=" CZ  ARG A 873 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.17   42.83     2      1.50e+01 4.44e-03 9.86e+00
  dihedral pdb=" CG  ARG B 873 "
           pdb=" CD  ARG B 873 "
           pdb=" NE  ARG B 873 "
           pdb=" CZ  ARG B 873 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.18   42.82     2      1.50e+01 4.44e-03 9.86e+00
  dihedral pdb=" CA  GLY A 453 "
           pdb=" C   GLY A 453 "
           pdb=" N   LYS A 454 "
           pdb=" CA  LYS A 454 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.39   15.61     0      5.00e+00 4.00e-02 9.75e+00
  ... (remaining 7471 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1066
       0.025 -    0.049: 432
       0.049 -    0.074: 212
       0.074 -    0.099: 57
       0.099 -    0.124: 53
  Chirality restraints: 1820
  Sorted by residual:
  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 3.82e-01
  chirality pdb=" CA  ILE A 685 "
            pdb=" N   ILE A 685 "
            pdb=" C   ILE A 685 "
            pdb=" CB  ILE A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  chirality pdb=" CA  ILE B 963 "
            pdb=" N   ILE B 963 "
            pdb=" C   ILE B 963 "
            pdb=" CB  ILE B 963 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 1817 not shown)

  Planarity restraints: 2142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 880 "   -0.051 5.00e-02 4.00e+02   7.64e-02 9.34e+00
        pdb=" N   PRO A 881 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 881 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 881 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 880 "    0.051 5.00e-02 4.00e+02   7.62e-02 9.28e+00
        pdb=" N   PRO B 881 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 881 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 881 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 930 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   ASN B 930 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ASN B 930 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 931 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2139 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 254
        2.71 -     3.26: 11750
        3.26 -     3.81: 19267
        3.81 -     4.35: 24778
        4.35 -     4.90: 42209
  Nonbonded interactions: 98258
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 979 "
            pdb=" OG  SER A 982 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   LYS B 979 "
            pdb=" OG  SER B 982 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   VAL B 838 "
            pdb=" NH2 ARG B1039 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   VAL A 838 "
            pdb=" NH2 ARG A1039 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OD1 ASP A 997 "
            pdb=" N   SER A 998 "
     model   vdw
     2.226 3.120
  ... (remaining 98253 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=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:                  0.010
  Normalize map: mean=0, sd=1:             2.510
  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:             0.020
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     35.990
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
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   0.065  12446  Z= 0.107
  Angle     :  0.498   7.241  16816  Z= 0.275
  Chirality :  0.037   0.124   1820
  Planarity :  0.004   0.076   2142
  Dihedral  : 15.113  84.780   4662
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.91 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.63 (0.22), residues: 1486
  helix:  1.47 (0.19), residues: 680
  sheet: -0.64 (0.38), residues: 212
  loop : -0.31 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1189 
 HIS   0.005   0.001   HIS A 650 
 PHE   0.007   0.001   PHE B 629 
 TYR   0.008   0.001   TYR A1079 
 ARG   0.007   0.000   ARG A1004 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15837 (  598)
  hydrogen bonds       : angle       6.51956 ( 1704)
  covalent geometry    : bond        0.00225 (12446)
  covalent geometry    : angle       0.49814 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 1.213 
Fit side-chains
REVERT: B  663 GLU cc_start: 0.6940 (tp30) cc_final: 0.6522 (tp30)
REVERT: A  663 GLU cc_start: 0.6923 (tp30) cc_final: 0.6504 (tp30)
  outliers start: 10
  outliers final: 2
  residues processed: 146
  average time/residue: 0.2585
  time to fit residues: 53.4258
Evaluate side-chains
  135 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  982 SER
Chi-restraints excluded: chain A residue  982 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.9980
   chunk 112 optimal weight:    0.2980
   chunk 62 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 116 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 134 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 623 HIS
B 887 HIS
B 892 HIS
A 623 HIS
A 887 HIS
A 892 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.148418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.111830 restraints weight = 13354.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.01
r_work: 0.2883 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12446  Z= 0.131
  Angle     :  0.499   8.274  16816  Z= 0.257
  Chirality :  0.039   0.141   1820
  Planarity :  0.004   0.052   2142
  Dihedral  :  3.614  16.451   1664
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.14 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.96 (0.22), residues: 1486
  helix:  1.77 (0.19), residues: 704
  sheet: -0.54 (0.38), residues: 216
  loop : -0.25 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1189 
 HIS   0.003   0.001   HIS A1051 
 PHE   0.009   0.001   PHE A 739 
 TYR   0.011   0.001   TYR B 837 
 ARG   0.005   0.001   ARG B1004 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  598)
  hydrogen bonds       : angle       4.76278 ( 1704)
  covalent geometry    : bond        0.00311 (12446)
  covalent geometry    : angle       0.49934 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 1.318 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6619 (m-40) cc_final: 0.6381 (m-40)
REVERT: B  997 ASP cc_start: 0.7699 (t0) cc_final: 0.7285 (t0)
REVERT: B 1019 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7966 (pptt)
REVERT: B 1080 GLU cc_start: 0.7905 (tt0) cc_final: 0.7252 (tp30)
REVERT: A  851 ASN cc_start: 0.6644 (m-40) cc_final: 0.6422 (m-40)
REVERT: A  997 ASP cc_start: 0.7717 (t0) cc_final: 0.7305 (t0)
REVERT: A 1019 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7965 (pptt)
REVERT: A 1080 GLU cc_start: 0.7914 (tt0) cc_final: 0.7279 (tp30)
  outliers start: 20
  outliers final: 14
  residues processed: 150
  average time/residue: 0.2659
  time to fit residues: 56.7443
Evaluate side-chains
  139 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  634 ASN
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  634 ASN
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 132 optimal weight:    0.5980
   chunk 145 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 111 optimal weight:    0.0070
   chunk 119 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   overall best weight:    0.9002

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.146495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.107969 restraints weight = 13625.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.39
r_work: 0.2806 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12446  Z= 0.137
  Angle     :  0.486   7.601  16816  Z= 0.251
  Chirality :  0.040   0.144   1820
  Planarity :  0.003   0.050   2142
  Dihedral  :  3.651  15.305   1662
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.13 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.22), residues: 1486
  helix:  1.95 (0.19), residues: 692
  sheet: -0.53 (0.37), residues: 228
  loop : -0.24 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1189 
 HIS   0.005   0.001   HIS B 609 
 PHE   0.009   0.001   PHE B 629 
 TYR   0.011   0.001   TYR A 920 
 ARG   0.003   0.000   ARG B1004 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  598)
  hydrogen bonds       : angle       4.47448 ( 1704)
  covalent geometry    : bond        0.00330 (12446)
  covalent geometry    : angle       0.48562 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 1.428 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6690 (m-40) cc_final: 0.6437 (m-40)
REVERT: B  997 ASP cc_start: 0.7767 (t0) cc_final: 0.7256 (t0)
REVERT: B 1019 LYS cc_start: 0.8134 (mttp) cc_final: 0.7870 (pptt)
REVERT: B 1046 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.6995 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8015 (tt0) cc_final: 0.7622 (mt-10)
REVERT: B 1080 GLU cc_start: 0.7786 (tt0) cc_final: 0.7185 (tp30)
REVERT: A  851 ASN cc_start: 0.6659 (m-40) cc_final: 0.6415 (m-40)
REVERT: A  997 ASP cc_start: 0.7793 (t0) cc_final: 0.7280 (t0)
REVERT: A 1019 LYS cc_start: 0.8158 (mttp) cc_final: 0.7889 (pptt)
REVERT: A 1046 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7011 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8043 (tt0) cc_final: 0.7620 (mt-10)
REVERT: A 1080 GLU cc_start: 0.7757 (tt0) cc_final: 0.7175 (tp30)
  outliers start: 22
  outliers final: 13
  residues processed: 154
  average time/residue: 0.2809
  time to fit residues: 61.3944
Evaluate side-chains
  137 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1100 THR
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0370
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.147530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.109911 restraints weight = 13349.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.95
r_work: 0.2939 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12446  Z= 0.110
  Angle     :  0.452   7.023  16816  Z= 0.234
  Chirality :  0.038   0.140   1820
  Planarity :  0.003   0.049   2142
  Dihedral  :  3.567  16.316   1662
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.36 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.18 (0.23), residues: 1486
  helix:  2.08 (0.20), residues: 692
  sheet: -0.43 (0.39), residues: 216
  loop : -0.26 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1189 
 HIS   0.005   0.001   HIS A 609 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.010   0.001   TYR B 920 
 ARG   0.003   0.000   ARG B1004 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  598)
  hydrogen bonds       : angle       4.26239 ( 1704)
  covalent geometry    : bond        0.00255 (12446)
  covalent geometry    : angle       0.45161 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 1.564 
Fit side-chains
   revert: symmetry clash
REVERT: B  851 ASN cc_start: 0.6758 (m-40) cc_final: 0.6448 (m-40)
REVERT: B  997 ASP cc_start: 0.7843 (t0) cc_final: 0.7304 (t0)
REVERT: B 1019 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7837 (pptt)
REVERT: B 1046 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7057 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8174 (tt0) cc_final: 0.7636 (mt-10)
REVERT: B 1080 GLU cc_start: 0.7858 (tt0) cc_final: 0.7233 (tp30)
REVERT: A  851 ASN cc_start: 0.6778 (m-40) cc_final: 0.6455 (m-40)
REVERT: A  997 ASP cc_start: 0.7857 (t0) cc_final: 0.7302 (t0)
REVERT: A 1019 LYS cc_start: 0.8199 (mttp) cc_final: 0.7862 (pptt)
REVERT: A 1073 GLU cc_start: 0.8168 (tt0) cc_final: 0.7637 (mt-10)
REVERT: A 1080 GLU cc_start: 0.7807 (tt0) cc_final: 0.7226 (tp30)
  outliers start: 20
  outliers final: 16
  residues processed: 150
  average time/residue: 0.4863
  time to fit residues: 103.4802
Evaluate side-chains
  142 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1097 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 125 optimal weight:    0.0670
   chunk 112 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 50 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.147744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.110584 restraints weight = 13403.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.15
r_work: 0.2884 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12446  Z= 0.103
  Angle     :  0.438   6.794  16816  Z= 0.228
  Chirality :  0.038   0.140   1820
  Planarity :  0.003   0.051   2142
  Dihedral  :  3.493  15.854   1662
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.28 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.29 (0.23), residues: 1486
  helix:  2.14 (0.19), residues: 704
  sheet: -0.43 (0.38), residues: 216
  loop : -0.19 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1189 
 HIS   0.004   0.001   HIS A 609 
 PHE   0.009   0.001   PHE A 710 
 TYR   0.010   0.001   TYR B 920 
 ARG   0.002   0.000   ARG A1004 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (  598)
  hydrogen bonds       : angle       4.14446 ( 1704)
  covalent geometry    : bond        0.00237 (12446)
  covalent geometry    : angle       0.43835 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.753 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6792 (m-40) cc_final: 0.6520 (m110)
REVERT: B  997 ASP cc_start: 0.7793 (t0) cc_final: 0.7220 (t0)
REVERT: B 1019 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7828 (pptt)
REVERT: B 1046 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7003 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8184 (tt0) cc_final: 0.7618 (mt-10)
REVERT: B 1080 GLU cc_start: 0.7814 (tt0) cc_final: 0.7206 (tp30)
REVERT: A  851 ASN cc_start: 0.6801 (m-40) cc_final: 0.6526 (m110)
REVERT: A  997 ASP cc_start: 0.7804 (t0) cc_final: 0.7237 (t0)
REVERT: A 1019 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7815 (pptt)
REVERT: A 1046 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7000 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8191 (tt0) cc_final: 0.7629 (mt-10)
REVERT: A 1080 GLU cc_start: 0.7781 (tt0) cc_final: 0.7205 (tp30)
  outliers start: 26
  outliers final: 18
  residues processed: 153
  average time/residue: 0.3114
  time to fit residues: 68.3727
Evaluate side-chains
  149 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1097 LEU
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1097 LEU
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.143560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.105156 restraints weight = 13656.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.61
r_work: 0.2800 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12446  Z= 0.201
  Angle     :  0.529   7.979  16816  Z= 0.275
  Chirality :  0.041   0.144   1820
  Planarity :  0.004   0.054   2142
  Dihedral  :  3.900  16.596   1662
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.36 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.99 (0.22), residues: 1486
  helix:  1.90 (0.19), residues: 702
  sheet: -0.71 (0.37), residues: 230
  loop : -0.27 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 820 
 HIS   0.004   0.001   HIS A1051 
 PHE   0.014   0.002   PHE B1191 
 TYR   0.013   0.002   TYR B 837 
 ARG   0.007   0.000   ARG A1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  598)
  hydrogen bonds       : angle       4.43655 ( 1704)
  covalent geometry    : bond        0.00499 (12446)
  covalent geometry    : angle       0.52886 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 1.740 
Fit side-chains
REVERT: B  928 GLN cc_start: 0.8149 (mp10) cc_final: 0.7843 (mp10)
REVERT: B  930 ASN cc_start: 0.8213 (t0) cc_final: 0.7616 (t0)
REVERT: B  997 ASP cc_start: 0.7817 (t0) cc_final: 0.7224 (t0)
REVERT: B 1019 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7813 (pptt)
REVERT: B 1046 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7042 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8188 (tt0) cc_final: 0.7923 (tt0)
REVERT: B 1080 GLU cc_start: 0.7730 (tt0) cc_final: 0.7230 (tp30)
REVERT: A  930 ASN cc_start: 0.8237 (t0) cc_final: 0.7649 (t0)
REVERT: A  997 ASP cc_start: 0.7812 (t0) cc_final: 0.7217 (t0)
REVERT: A 1019 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7797 (pptt)
REVERT: A 1046 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7065 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8188 (tt0) cc_final: 0.7923 (tt0)
REVERT: A 1080 GLU cc_start: 0.7723 (tt0) cc_final: 0.7236 (tp30)
  outliers start: 25
  outliers final: 17
  residues processed: 147
  average time/residue: 0.3176
  time to fit residues: 67.7254
Evaluate side-chains
  143 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  909 HIS
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0870
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.145090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.106139 restraints weight = 13592.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 2.35
r_work: 0.2815 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12446  Z= 0.164
  Angle     :  0.497   7.696  16816  Z= 0.258
  Chirality :  0.040   0.140   1820
  Planarity :  0.004   0.054   2142
  Dihedral  :  3.805  15.276   1662
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.12 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.99 (0.22), residues: 1486
  helix:  1.92 (0.19), residues: 702
  sheet: -0.75 (0.37), residues: 228
  loop : -0.27 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1189 
 HIS   0.003   0.001   HIS B1051 
 PHE   0.015   0.001   PHE B 959 
 TYR   0.015   0.001   TYR B 580 
 ARG   0.005   0.000   ARG A1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  598)
  hydrogen bonds       : angle       4.36092 ( 1704)
  covalent geometry    : bond        0.00404 (12446)
  covalent geometry    : angle       0.49680 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 2.133 
Fit side-chains
REVERT: B  566 HIS cc_start: 0.7719 (m170) cc_final: 0.7512 (t-170)
REVERT: B  928 GLN cc_start: 0.8174 (mp10) cc_final: 0.7874 (mp10)
REVERT: B  930 ASN cc_start: 0.8201 (t0) cc_final: 0.7589 (t0)
REVERT: B  997 ASP cc_start: 0.7792 (t0) cc_final: 0.7184 (t0)
REVERT: B 1019 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7812 (pptt)
REVERT: B 1046 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7120 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8267 (tt0) cc_final: 0.8007 (tt0)
REVERT: B 1080 GLU cc_start: 0.7771 (tt0) cc_final: 0.7197 (tp30)
REVERT: A  420 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7281 (ptm-80)
REVERT: A  566 HIS cc_start: 0.7730 (m170) cc_final: 0.7530 (t-170)
REVERT: A  928 GLN cc_start: 0.8193 (mp10) cc_final: 0.7874 (mp10)
REVERT: A  930 ASN cc_start: 0.8220 (t0) cc_final: 0.7608 (t0)
REVERT: A  997 ASP cc_start: 0.7797 (t0) cc_final: 0.7188 (t0)
REVERT: A 1019 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7806 (pptt)
REVERT: A 1046 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7139 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8284 (tt0) cc_final: 0.8028 (tt0)
REVERT: A 1080 GLU cc_start: 0.7799 (tt0) cc_final: 0.7229 (tp30)
  outliers start: 24
  outliers final: 20
  residues processed: 158
  average time/residue: 0.3125
  time to fit residues: 73.0499
Evaluate side-chains
  152 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 2.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  909 HIS
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 109 optimal weight:    0.4980
   chunk 56 optimal weight:    0.3980
   chunk 90 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.147082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.108703 restraints weight = 13642.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.24
r_work: 0.2835 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12446  Z= 0.111
  Angle     :  0.454   7.185  16816  Z= 0.237
  Chirality :  0.038   0.140   1820
  Planarity :  0.003   0.055   2142
  Dihedral  :  3.628  15.072   1662
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.27 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.14 (0.23), residues: 1486
  helix:  2.03 (0.19), residues: 704
  sheet: -0.70 (0.37), residues: 228
  loop : -0.19 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1189 
 HIS   0.003   0.001   HIS B 609 
 PHE   0.014   0.001   PHE A 959 
 TYR   0.012   0.001   TYR B 580 
 ARG   0.005   0.000   ARG B1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  598)
  hydrogen bonds       : angle       4.18928 ( 1704)
  covalent geometry    : bond        0.00259 (12446)
  covalent geometry    : angle       0.45368 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.404 
Fit side-chains
REVERT: B  652 TYR cc_start: 0.8334 (m-80) cc_final: 0.8041 (m-80)
REVERT: B  928 GLN cc_start: 0.8128 (mp10) cc_final: 0.7848 (mp10)
REVERT: B  997 ASP cc_start: 0.7817 (t0) cc_final: 0.7204 (t0)
REVERT: B 1019 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7840 (pptt)
REVERT: B 1046 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7065 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8243 (tt0) cc_final: 0.8001 (tt0)
REVERT: B 1080 GLU cc_start: 0.7764 (tt0) cc_final: 0.7257 (tp30)
REVERT: A  420 ARG cc_start: 0.7865 (ptm160) cc_final: 0.7309 (ptm-80)
REVERT: A  652 TYR cc_start: 0.8318 (m-80) cc_final: 0.7944 (m-80)
REVERT: A  928 GLN cc_start: 0.8173 (mp10) cc_final: 0.7882 (mp10)
REVERT: A  930 ASN cc_start: 0.8278 (t0) cc_final: 0.7643 (t0)
REVERT: A  997 ASP cc_start: 0.7818 (t0) cc_final: 0.7204 (t0)
REVERT: A 1019 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7842 (pptt)
REVERT: A 1046 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7053 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8272 (tt0) cc_final: 0.8037 (tt0)
REVERT: A 1080 GLU cc_start: 0.7802 (tt0) cc_final: 0.7275 (tp30)
  outliers start: 21
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2664
  time to fit residues: 57.3807
Evaluate side-chains
  148 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  964 ILE
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 138 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 136 optimal weight:    3.9990
   chunk 137 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0570
   chunk 120 optimal weight:    0.9990
   overall best weight:    0.8502

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
B 930 ASN
A 892 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.146348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.108140 restraints weight = 13526.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.29
r_work: 0.2852 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12446  Z= 0.130
  Angle     :  0.468   7.426  16816  Z= 0.244
  Chirality :  0.039   0.141   1820
  Planarity :  0.004   0.056   2142
  Dihedral  :  3.637  14.746   1662
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.66 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.11 (0.23), residues: 1486
  helix:  2.04 (0.19), residues: 704
  sheet: -0.77 (0.37), residues: 230
  loop : -0.20 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1189 
 HIS   0.003   0.001   HIS A1192 
 PHE   0.014   0.001   PHE A 959 
 TYR   0.015   0.001   TYR A 580 
 ARG   0.005   0.000   ARG A1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  598)
  hydrogen bonds       : angle       4.20963 ( 1704)
  covalent geometry    : bond        0.00315 (12446)
  covalent geometry    : angle       0.46766 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 1.264 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6791 (m-40) cc_final: 0.6413 (m110)
REVERT: B  928 GLN cc_start: 0.8131 (mp10) cc_final: 0.7848 (mp10)
REVERT: B  997 ASP cc_start: 0.7754 (t0) cc_final: 0.7146 (t0)
REVERT: B 1019 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7813 (pptt)
REVERT: B 1046 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7073 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8242 (tt0) cc_final: 0.7991 (tt0)
REVERT: B 1080 GLU cc_start: 0.7766 (tt0) cc_final: 0.7208 (tp30)
REVERT: A  420 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7329 (ptm-80)
REVERT: A  851 ASN cc_start: 0.6762 (m-40) cc_final: 0.6398 (m110)
REVERT: A  928 GLN cc_start: 0.8185 (mp10) cc_final: 0.7894 (mp10)
REVERT: A  930 ASN cc_start: 0.8233 (t0) cc_final: 0.7586 (t0)
REVERT: A  997 ASP cc_start: 0.7748 (t0) cc_final: 0.7141 (t0)
REVERT: A 1019 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7813 (pptt)
REVERT: A 1046 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7109 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8255 (tt0) cc_final: 0.8015 (tt0)
REVERT: A 1080 GLU cc_start: 0.7763 (tt0) cc_final: 0.7240 (tp30)
  outliers start: 27
  outliers final: 22
  residues processed: 158
  average time/residue: 0.2524
  time to fit residues: 57.1691
Evaluate side-chains
  155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  909 HIS
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 119 optimal weight:    0.4980
   chunk 141 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
B 930 ASN
A 892 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.146454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.108027 restraints weight = 13514.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.46
r_work: 0.2835 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12446  Z= 0.132
  Angle     :  0.469   7.580  16816  Z= 0.244
  Chirality :  0.039   0.141   1820
  Planarity :  0.004   0.056   2142
  Dihedral  :  3.644  14.669   1662
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.89 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.11 (0.23), residues: 1486
  helix:  2.03 (0.19), residues: 704
  sheet: -0.75 (0.37), residues: 228
  loop : -0.23 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A1192 
 PHE   0.014   0.001   PHE A 959 
 TYR   0.014   0.001   TYR A 580 
 ARG   0.005   0.000   ARG B1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03600 (  598)
  hydrogen bonds       : angle       4.19823 ( 1704)
  covalent geometry    : bond        0.00320 (12446)
  covalent geometry    : angle       0.46903 (16816)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.511 
Fit side-chains
REVERT: B  420 ARG cc_start: 0.7949 (ptm160) cc_final: 0.7420 (ptm-80)
REVERT: B  928 GLN cc_start: 0.8111 (mp10) cc_final: 0.7829 (mp10)
REVERT: B  997 ASP cc_start: 0.7797 (t0) cc_final: 0.7195 (t0)
REVERT: B 1019 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7846 (pptt)
REVERT: B 1046 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7098 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8254 (tt0) cc_final: 0.8000 (tt0)
REVERT: B 1080 GLU cc_start: 0.7777 (tt0) cc_final: 0.7262 (tp30)
REVERT: A  928 GLN cc_start: 0.8162 (mp10) cc_final: 0.7875 (mp10)
REVERT: A  930 ASN cc_start: 0.8265 (t0) cc_final: 0.7633 (t0)
REVERT: A  997 ASP cc_start: 0.7801 (t0) cc_final: 0.7198 (t0)
REVERT: A 1019 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7843 (pptt)
REVERT: A 1046 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7098 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8282 (tt0) cc_final: 0.8034 (tt0)
REVERT: A 1080 GLU cc_start: 0.7806 (tt0) cc_final: 0.7283 (tp30)
  outliers start: 26
  outliers final: 22
  residues processed: 156
  average time/residue: 0.3551
  time to fit residues: 78.8996
Evaluate side-chains
  154 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  571 ARG
Chi-restraints excluded: chain B residue  588 VAL
Chi-restraints excluded: chain B residue  636 VAL
Chi-restraints excluded: chain B residue  672 THR
Chi-restraints excluded: chain B residue  735 GLU
Chi-restraints excluded: chain B residue  773 SER
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  909 HIS
Chi-restraints excluded: chain B residue 1019 LYS
Chi-restraints excluded: chain B residue 1046 ARG
Chi-restraints excluded: chain B residue 1127 SER
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  735 GLU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  909 HIS
Chi-restraints excluded: chain A residue 1019 LYS
Chi-restraints excluded: chain A residue 1046 ARG
Chi-restraints excluded: chain A residue 1127 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0670
   chunk 98 optimal weight:    0.0170
   chunk 76 optimal weight:    0.9980
   chunk 133 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 146 optimal weight:    0.7980
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
B 930 ASN
A 892 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.148295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.110176 restraints weight = 13514.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.21
r_work: 0.2884 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12446  Z= 0.098
  Angle     :  0.439   7.125  16816  Z= 0.229
  Chirality :  0.038   0.138   1820
  Planarity :  0.003   0.055   2142
  Dihedral  :  3.494  13.874   1662
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.89 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.25 (0.23), residues: 1486
  helix:  2.17 (0.20), residues: 704
  sheet: -0.68 (0.37), residues: 228
  loop : -0.20 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1189 
 HIS   0.007   0.001   HIS A 566 
 PHE   0.015   0.001   PHE B 959 
 TYR   0.012   0.001   TYR A 580 
 ARG   0.005   0.000   ARG B1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03284 (  598)
  hydrogen bonds       : angle       4.06950 ( 1704)
  covalent geometry    : bond        0.00225 (12446)
  covalent geometry    : angle       0.43900 (16816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7125.52 seconds
wall clock time: 128 minutes 33.27 seconds (7713.27 seconds total)