Starting phenix.real_space_refine
on Sat Aug 23 13:04:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9y_36119/08_2025/8j9y_36119.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9y_36119/08_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_36119/08_2025/8j9y_36119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9y_36119/08_2025/8j9y_36119.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9y_36119/08_2025/8j9y_36119.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9y_36119/08_2025/8j9y_36119.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.045
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12154
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      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:
    A
  Time building chain proxies: 5.05, per 1000 atoms: 0.42
  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: 0.71
  Conformation dependent library (CDL) restraints added in 393.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.29
  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: 1.65

  Time building geometry restraints manager: 0.99 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.220
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.780
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (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
 ARG   0.007   0.000   ARG A1004 
 TYR   0.008   0.001   TYR A1079 
 PHE   0.007   0.001   PHE B 629 
 TRP   0.007   0.001   TRP B1189 
 HIS   0.005   0.001   HIS A 650 

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

*********************** 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  : 0.436 
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: 0.1328
  time to fit residues: 27.4586
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  : 0.514 
-------------------------------------------------------------------------------
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 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.148182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.110877 restraints weight = 13515.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.15
r_work: 0.2863 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1150

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= 0.133
  Angle     :  0.503   8.191  16816  Z= 0.259
  Chirality :  0.040   0.143   1820
  Planarity :  0.004   0.053   2142
  Dihedral  :  3.653  16.459   1664
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.39
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.22), residues: 1486
  helix:  1.76 (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
 ARG   0.005   0.001   ARG B1004 
 TYR   0.011   0.001   TYR A 837 
 PHE   0.009   0.001   PHE A 629 
 TRP   0.008   0.001   TRP A 820 
 HIS   0.003   0.001   HIS A1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (12446)
  covalent geometry    : angle       0.50296 (16816)
  hydrogen bonds       : bond        0.03735 (  598)
  hydrogen bonds       : angle       4.74138 ( 1704)

*********************** 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
  157 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.507 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6666 (m-40) cc_final: 0.6408 (m-40)
REVERT: B  997 ASP cc_start: 0.7712 (t0) cc_final: 0.7303 (t0)
REVERT: B 1019 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7971 (pptt)
REVERT: B 1080 GLU cc_start: 0.7938 (tt0) cc_final: 0.7287 (tp30)
REVERT: A  851 ASN cc_start: 0.6746 (m-40) cc_final: 0.6496 (m-40)
REVERT: A  997 ASP cc_start: 0.7732 (t0) cc_final: 0.7310 (t0)
REVERT: A 1019 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7976 (pptt)
  outliers start: 20
  outliers final: 14
  residues processed: 151
  average time/residue: 0.1251
  time to fit residues: 27.0701
Evaluate side-chains
  138 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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 61 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 140 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 132 optimal weight:    0.5980
   chunk 126 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 129 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.145565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.107597 restraints weight = 13651.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.51
r_work: 0.2783 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12446  Z= 0.154
  Angle     :  0.500   7.764  16816  Z= 0.258
  Chirality :  0.040   0.144   1820
  Planarity :  0.004   0.050   2142
  Dihedral  :  3.713  15.337   1662
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.22), residues: 1486
  helix:  1.89 (0.19), residues: 692
  sheet: -0.57 (0.37), residues: 228
  loop : -0.25 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1004 
 TYR   0.011   0.001   TYR B 920 
 PHE   0.009   0.001   PHE B 629 
 TRP   0.009   0.001   TRP B1189 
 HIS   0.004   0.001   HIS B 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12446)
  covalent geometry    : angle       0.49999 (16816)
  hydrogen bonds       : bond        0.03909 (  598)
  hydrogen bonds       : angle       4.52718 ( 1704)

*********************** 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
  162 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.519 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6728 (m-40) cc_final: 0.6455 (m-40)
REVERT: B  997 ASP cc_start: 0.7775 (t0) cc_final: 0.7258 (t0)
REVERT: B 1019 LYS cc_start: 0.8155 (mttp) cc_final: 0.7873 (pptt)
REVERT: B 1046 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7018 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8031 (tt0) cc_final: 0.7630 (mt-10)
REVERT: B 1080 GLU cc_start: 0.7803 (tt0) cc_final: 0.7189 (tp30)
REVERT: A  851 ASN cc_start: 0.6728 (m-40) cc_final: 0.6463 (m-40)
REVERT: A  997 ASP cc_start: 0.7796 (t0) cc_final: 0.7277 (t0)
REVERT: A 1019 LYS cc_start: 0.8175 (mttp) cc_final: 0.7900 (pptt)
REVERT: A 1046 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7028 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8056 (tt0) cc_final: 0.7626 (mt-10)
REVERT: A 1080 GLU cc_start: 0.7925 (tm-30) cc_final: 0.6715 (tp30)
  outliers start: 23
  outliers final: 15
  residues processed: 159
  average time/residue: 0.1332
  time to fit residues: 29.8652
Evaluate side-chains
  140 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  461 SER
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 1097 LEU
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 121 optimal weight:    0.0870
   chunk 53 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 47 optimal weight:    0.2980
   chunk 99 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 141 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.147989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.109590 restraints weight = 13499.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.34
r_work: 0.2867 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1617

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= 0.113
  Angle     :  0.457   7.089  16816  Z= 0.237
  Chirality :  0.039   0.139   1820
  Planarity :  0.003   0.048   2142
  Dihedral  :  3.599  16.360   1662
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.36 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.23), residues: 1486
  helix:  2.04 (0.20), residues: 692
  sheet: -0.47 (0.37), residues: 228
  loop : -0.23 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1004 
 TYR   0.010   0.001   TYR A 920 
 PHE   0.009   0.001   PHE B 710 
 TRP   0.011   0.001   TRP B1189 
 HIS   0.005   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12446)
  covalent geometry    : angle       0.45728 (16816)
  hydrogen bonds       : bond        0.03482 (  598)
  hydrogen bonds       : angle       4.29790 ( 1704)

*********************** 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
  159 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.481 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6737 (m-40) cc_final: 0.6348 (m-40)
REVERT: B  997 ASP cc_start: 0.7711 (t0) cc_final: 0.7161 (t0)
REVERT: B 1019 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7744 (pptt)
REVERT: B 1046 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7076 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8195 (tt0) cc_final: 0.7620 (mt-10)
REVERT: B 1080 GLU cc_start: 0.7823 (tt0) cc_final: 0.7146 (tp30)
REVERT: A  851 ASN cc_start: 0.6693 (m-40) cc_final: 0.6349 (m-40)
REVERT: A  997 ASP cc_start: 0.7726 (t0) cc_final: 0.7173 (t0)
REVERT: A 1019 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7743 (pptt)
REVERT: A 1046 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7122 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8196 (tt0) cc_final: 0.7629 (mt-10)
REVERT: A 1080 GLU cc_start: 0.8024 (tm-30) cc_final: 0.6751 (tp30)
  outliers start: 24
  outliers final: 16
  residues processed: 152
  average time/residue: 0.1115
  time to fit residues: 24.0541
Evaluate side-chains
  144 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 126 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 105 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.145914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.107239 restraints weight = 13614.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 2.26
r_work: 0.2816 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12446  Z= 0.151
  Angle     :  0.484   7.463  16816  Z= 0.251
  Chirality :  0.040   0.143   1820
  Planarity :  0.003   0.052   2142
  Dihedral  :  3.707  15.502   1662
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.82 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.22), residues: 1486
  helix:  1.99 (0.19), residues: 704
  sheet: -0.54 (0.37), residues: 228
  loop : -0.23 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1004 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.010   0.001   PHE B 596 
 TRP   0.011   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (12446)
  covalent geometry    : angle       0.48374 (16816)
  hydrogen bonds       : bond        0.03772 (  598)
  hydrogen bonds       : angle       4.33429 ( 1704)

*********************** 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
  159 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.476 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6763 (m-40) cc_final: 0.6458 (m110)
REVERT: B  997 ASP cc_start: 0.7789 (t0) cc_final: 0.7216 (t0)
REVERT: B 1019 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7797 (pptt)
REVERT: B 1046 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7112 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8186 (tt0) cc_final: 0.7623 (mt-10)
REVERT: B 1080 GLU cc_start: 0.7774 (tt0) cc_final: 0.7237 (tp30)
REVERT: A  851 ASN cc_start: 0.6788 (m-40) cc_final: 0.6490 (m110)
REVERT: A  997 ASP cc_start: 0.7801 (t0) cc_final: 0.7228 (t0)
REVERT: A 1019 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7802 (pptt)
REVERT: A 1046 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7134 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8213 (tt0) cc_final: 0.7651 (mt-10)
REVERT: A 1080 GLU cc_start: 0.8133 (tm-30) cc_final: 0.6906 (tp30)
  outliers start: 24
  outliers final: 15
  residues processed: 153
  average time/residue: 0.1357
  time to fit residues: 29.2407
Evaluate side-chains
  146 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
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 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 1127 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 112 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 147 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 46 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
B 456 ASN
B 892 HIS
A 892 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.144747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.106157 restraints weight = 13686.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.28
r_work: 0.2831 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12446  Z= 0.176
  Angle     :  0.506   7.851  16816  Z= 0.263
  Chirality :  0.040   0.142   1820
  Planarity :  0.004   0.053   2142
  Dihedral  :  3.816  15.312   1662
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.27 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.22), residues: 1486
  helix:  1.94 (0.19), residues: 702
  sheet: -0.69 (0.37), residues: 228
  loop : -0.28 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 428 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.012   0.001   PHE B1191 
 TRP   0.012   0.001   TRP A1189 
 HIS   0.004   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12446)
  covalent geometry    : angle       0.50606 (16816)
  hydrogen bonds       : bond        0.03929 (  598)
  hydrogen bonds       : angle       4.37826 ( 1704)

*********************** 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
  155 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.509 
Fit side-chains
REVERT: B  928 GLN cc_start: 0.8179 (mp10) cc_final: 0.7869 (mp10)
REVERT: B  997 ASP cc_start: 0.7826 (t0) cc_final: 0.7229 (t0)
REVERT: B 1019 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7855 (pptt)
REVERT: B 1046 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7143 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8232 (tt0) cc_final: 0.7982 (tt0)
REVERT: B 1080 GLU cc_start: 0.7834 (tt0) cc_final: 0.7271 (tp30)
REVERT: A  928 GLN cc_start: 0.8200 (mp10) cc_final: 0.7901 (mp10)
REVERT: A  930 ASN cc_start: 0.8252 (t0) cc_final: 0.7663 (t0)
REVERT: A  997 ASP cc_start: 0.7838 (t0) cc_final: 0.7240 (t0)
REVERT: A 1019 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7853 (pptt)
REVERT: A 1046 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7168 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8247 (tt0) cc_final: 0.7998 (tt0)
REVERT: A 1080 GLU cc_start: 0.8175 (tm-30) cc_final: 0.6976 (tp30)
  outliers start: 25
  outliers final: 19
  residues processed: 152
  average time/residue: 0.1265
  time to fit residues: 27.6532
Evaluate side-chains
  151 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 133 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 109 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 129 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 892 HIS
B 984 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 = 0.3565 r_free = 0.3565 target = 0.147195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.108625 restraints weight = 13472.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.20
r_work: 0.2870 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1983

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= 0.105
  Angle     :  0.448   6.892  16816  Z= 0.234
  Chirality :  0.038   0.140   1820
  Planarity :  0.003   0.054   2142
  Dihedral  :  3.604  15.423   1662
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.89 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.23), residues: 1486
  helix:  2.09 (0.20), residues: 704
  sheet: -0.69 (0.37), residues: 230
  loop : -0.15 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1057 
 TYR   0.011   0.001   TYR B 580 
 PHE   0.015   0.001   PHE B 959 
 TRP   0.013   0.001   TRP A1189 
 HIS   0.003   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (12446)
  covalent geometry    : angle       0.44824 (16816)
  hydrogen bonds       : bond        0.03415 (  598)
  hydrogen bonds       : angle       4.17103 ( 1704)

*********************** 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
  158 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.514 
Fit side-chains
REVERT: B  652 TYR cc_start: 0.8237 (m-80) cc_final: 0.7937 (m-80)
REVERT: B  851 ASN cc_start: 0.6710 (m-40) cc_final: 0.6347 (m110)
REVERT: B  928 GLN cc_start: 0.8169 (mp10) cc_final: 0.7870 (mp10)
REVERT: B  997 ASP cc_start: 0.7742 (t0) cc_final: 0.7120 (t0)
REVERT: B 1019 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7789 (pptt)
REVERT: B 1046 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7023 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8225 (tt0) cc_final: 0.7981 (tt0)
REVERT: B 1080 GLU cc_start: 0.7759 (tt0) cc_final: 0.7238 (tp30)
REVERT: A  420 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7227 (ptm-80)
REVERT: A  652 TYR cc_start: 0.8229 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  851 ASN cc_start: 0.6691 (m-40) cc_final: 0.6354 (m110)
REVERT: A  928 GLN cc_start: 0.8187 (mp10) cc_final: 0.7890 (mp10)
REVERT: A  930 ASN cc_start: 0.8206 (t0) cc_final: 0.7586 (t0)
REVERT: A  997 ASP cc_start: 0.7772 (t0) cc_final: 0.7149 (t0)
REVERT: A 1019 LYS cc_start: 0.8125 (mttp) cc_final: 0.7789 (pptt)
REVERT: A 1046 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7046 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8252 (tt0) cc_final: 0.8014 (tt0)
REVERT: A 1080 GLU cc_start: 0.8126 (tm-30) cc_final: 0.6919 (tp30)
  outliers start: 20
  outliers final: 17
  residues processed: 157
  average time/residue: 0.1270
  time to fit residues: 28.5073
Evaluate side-chains
  150 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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 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 72 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 98 optimal weight:    1.9990
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.146425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.108208 restraints weight = 13487.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.26
r_work: 0.2827 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12446  Z= 0.125
  Angle     :  0.461   7.242  16816  Z= 0.240
  Chirality :  0.039   0.141   1820
  Planarity :  0.003   0.055   2142
  Dihedral  :  3.618  15.094   1662
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.35 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.23), residues: 1486
  helix:  2.08 (0.19), residues: 704
  sheet: -0.73 (0.37), residues: 230
  loop : -0.18 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1057 
 TYR   0.015   0.001   TYR A 580 
 PHE   0.013   0.001   PHE A 959 
 TRP   0.012   0.001   TRP A1189 
 HIS   0.006   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (12446)
  covalent geometry    : angle       0.46079 (16816)
  hydrogen bonds       : bond        0.03527 (  598)
  hydrogen bonds       : angle       4.17767 ( 1704)

*********************** 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
  156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.528 
Fit side-chains
REVERT: B  851 ASN cc_start: 0.6787 (m-40) cc_final: 0.6419 (m110)
REVERT: B  928 GLN cc_start: 0.8142 (mp10) cc_final: 0.7861 (mp10)
REVERT: B  997 ASP cc_start: 0.7808 (t0) cc_final: 0.7191 (t0)
REVERT: B 1019 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7823 (pptt)
REVERT: B 1046 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7045 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8230 (tt0) cc_final: 0.7991 (tt0)
REVERT: B 1080 GLU cc_start: 0.7834 (tt0) cc_final: 0.7289 (tp30)
REVERT: A  420 ARG cc_start: 0.7914 (ptm160) cc_final: 0.7334 (ptm-80)
REVERT: A  851 ASN cc_start: 0.6766 (m-40) cc_final: 0.6401 (m110)
REVERT: A  928 GLN cc_start: 0.8164 (mp10) cc_final: 0.7888 (mp10)
REVERT: A  997 ASP cc_start: 0.7815 (t0) cc_final: 0.7196 (t0)
REVERT: A 1019 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7825 (pptt)
REVERT: A 1046 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7063 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8254 (tt0) cc_final: 0.8020 (tt0)
REVERT: A 1080 GLU cc_start: 0.8114 (tm-30) cc_final: 0.6937 (tp30)
  outliers start: 26
  outliers final: 22
  residues processed: 154
  average time/residue: 0.1156
  time to fit residues: 25.4319
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  : 0.477 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 111 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 105 optimal weight:    0.5980
   chunk 130 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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
A 930 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.145535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.107073 restraints weight = 13597.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.23
r_work: 0.2849 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12446  Z= 0.144
  Angle     :  0.476   7.516  16816  Z= 0.249
  Chirality :  0.039   0.141   1820
  Planarity :  0.004   0.055   2142
  Dihedral  :  3.686  14.973   1662
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.74 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.23), residues: 1486
  helix:  2.03 (0.19), residues: 704
  sheet: -0.80 (0.37), residues: 230
  loop : -0.20 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1057 
 TYR   0.016   0.001   TYR A 580 
 PHE   0.012   0.001   PHE A 959 
 TRP   0.012   0.001   TRP A1189 
 HIS   0.003   0.001   HIS B1051 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12446)
  covalent geometry    : angle       0.47613 (16816)
  hydrogen bonds       : bond        0.03692 (  598)
  hydrogen bonds       : angle       4.24049 ( 1704)

*********************** 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
  163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.529 
Fit side-chains
REVERT: B  928 GLN cc_start: 0.8135 (mp10) cc_final: 0.7849 (mp10)
REVERT: B  997 ASP cc_start: 0.7812 (t0) cc_final: 0.7207 (t0)
REVERT: B 1019 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7863 (pptt)
REVERT: B 1046 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7108 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8254 (tt0) cc_final: 0.8009 (tt0)
REVERT: B 1080 GLU cc_start: 0.7833 (tt0) cc_final: 0.7294 (tp30)
REVERT: A  928 GLN cc_start: 0.8158 (mp10) cc_final: 0.7883 (mp10)
REVERT: A  930 ASN cc_start: 0.8372 (t0) cc_final: 0.7657 (t0)
REVERT: A  997 ASP cc_start: 0.7828 (t0) cc_final: 0.7226 (t0)
REVERT: A 1019 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7857 (pptt)
REVERT: A 1046 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7127 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8283 (tt0) cc_final: 0.8042 (tt0)
REVERT: A 1080 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7005 (tp30)
  outliers start: 31
  outliers final: 25
  residues processed: 160
  average time/residue: 0.1245
  time to fit residues: 28.5697
Evaluate side-chains
  156 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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 1100 THR
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  895 THR
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 1100 THR
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 72 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 138 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 147 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 145 optimal weight:    0.1980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.146687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.108345 restraints weight = 13505.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.30
r_work: 0.2855 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12446  Z= 0.118
  Angle     :  0.457   7.406  16816  Z= 0.238
  Chirality :  0.039   0.140   1820
  Planarity :  0.003   0.055   2142
  Dihedral  :  3.603  14.424   1662
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.05 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.23), residues: 1486
  helix:  2.09 (0.19), residues: 704
  sheet: -0.73 (0.37), residues: 228
  loop : -0.19 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1057 
 TYR   0.014   0.001   TYR A 580 
 PHE   0.016   0.001   PHE A 959 
 TRP   0.012   0.001   TRP A1189 
 HIS   0.007   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12446)
  covalent geometry    : angle       0.45698 (16816)
  hydrogen bonds       : bond        0.03494 (  598)
  hydrogen bonds       : angle       4.14281 ( 1704)

********************** 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
  167 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.521 
Fit side-chains
REVERT: B  420 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7423 (ptm-80)
REVERT: B  652 TYR cc_start: 0.8256 (m-80) cc_final: 0.7828 (m-80)
REVERT: B  851 ASN cc_start: 0.6761 (m-40) cc_final: 0.6374 (m110)
REVERT: B  928 GLN cc_start: 0.8116 (mp10) cc_final: 0.7847 (mp10)
REVERT: B  997 ASP cc_start: 0.7743 (t0) cc_final: 0.7131 (t0)
REVERT: B 1019 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7815 (pptt)
REVERT: B 1046 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7058 (ttt180)
REVERT: B 1073 GLU cc_start: 0.8254 (tt0) cc_final: 0.8001 (tt0)
REVERT: B 1080 GLU cc_start: 0.7793 (tt0) cc_final: 0.7264 (tp30)
REVERT: A  652 TYR cc_start: 0.8279 (m-80) cc_final: 0.7839 (m-80)
REVERT: A  851 ASN cc_start: 0.6737 (m-40) cc_final: 0.6360 (m110)
REVERT: A  928 GLN cc_start: 0.8155 (mp10) cc_final: 0.7894 (mp10)
REVERT: A  997 ASP cc_start: 0.7766 (t0) cc_final: 0.7153 (t0)
REVERT: A 1019 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7815 (pptt)
REVERT: A 1046 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7073 (ttt180)
REVERT: A 1073 GLU cc_start: 0.8288 (tt0) cc_final: 0.8041 (tt0)
REVERT: A 1080 GLU cc_start: 0.8115 (tm-30) cc_final: 0.6938 (tp30)
  outliers start: 28
  outliers final: 24
  residues processed: 163
  average time/residue: 0.1357
  time to fit residues: 30.8184
Evaluate side-chains
  161 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
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  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  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  895 THR
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 19 optimal weight:    0.8980
   chunk 95 optimal weight:    0.2980
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0010
   chunk 89 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 129 optimal weight:    0.7980
   chunk 147 optimal weight:    1.9990
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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
A 930 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.148120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.108915 restraints weight = 13443.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.08
r_work: 0.2896 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2085

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= 0.099
  Angle     :  0.437   7.329  16816  Z= 0.228
  Chirality :  0.038   0.138   1820
  Planarity :  0.003   0.055   2142
  Dihedral  :  3.484  13.790   1662
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.35 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.23), residues: 1486
  helix:  2.18 (0.20), residues: 704
  sheet: -0.65 (0.38), residues: 218
  loop : -0.18 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1057 
 TYR   0.013   0.001   TYR A 580 
 PHE   0.015   0.001   PHE A 959 
 TRP   0.011   0.001   TRP A1189 
 HIS   0.003   0.001   HIS A1192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (12446)
  covalent geometry    : angle       0.43721 (16816)
  hydrogen bonds       : bond        0.03303 (  598)
  hydrogen bonds       : angle       4.05215 ( 1704)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3259.89 seconds
wall clock time: 56 minutes 36.34 seconds (3396.34 seconds total)