Starting phenix.real_space_refine
on Tue Feb 11 15:03:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6npj_0471/02_2025/6npj_0471.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6npj_0471/02_2025/6npj_0471.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6npj_0471/02_2025/6npj_0471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6npj_0471/02_2025/6npj_0471.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6npj_0471/02_2025/6npj_0471.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6npj_0471/02_2025/6npj_0471.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.012
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      30      5.16       5
     C    3936      2.51       5
     N    1102      2.21       5
     O    1118      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6186
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3093
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 371}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3093
          Classifications: {'peptide': 384}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 371}
          Chain breaks: 1
  Time building chain proxies: 3.96, per 1000 atoms: 0.64
  Number of scatterers: 6186
  At special positions: 0
  Unit cell: (116.05, 88.62, 87.565, 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      30     16.00
     O    1118      8.00
     N    1102      7.00
     C    3936      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: 1.27
  Conformation dependent library (CDL) restraints added in 871.6 milliseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 4 sheets defined
      43.4% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'C' and resid 687 through 704
      removed outlier: 3.753A  pdb=" N   HIS C 693 " --> pdb=" O   ALA C 689 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER C 699 " --> pdb=" O   ALA C 695 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 706 through 710
      removed outlier: 4.018A  pdb=" N   LYS C 710 " --> pdb=" O   ASP C 707 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 727 through 733
      removed outlier: 3.870A  pdb=" N   VAL C 733 " --> pdb=" O   ILE C 729 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 756 through 761
      removed outlier: 3.685A  pdb=" N   LEU C 760 " --> pdb=" O   ASN C 756 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN C 761 " --> pdb=" O   PHE C 757 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 756 through 761'
    Processing helix  chain 'C' and resid 761 through 774
      removed outlier: 3.612A  pdb=" N   ARG C 766 " --> pdb=" O   SER C 762 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TYR C 767 " --> pdb=" O   ASP C 763 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 787 through 798
      removed outlier: 3.898A  pdb=" N   TYR C 794 " --> pdb=" O   GLN C 790 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   MET C 795 " --> pdb=" O   GLY C 791 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN C 797 " --> pdb=" O   GLN C 793 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 821 through 824
    Processing helix  chain 'C' and resid 825 through 836
    Processing helix  chain 'C' and resid 929 through 937
      removed outlier: 3.690A  pdb=" N   LEU C 934 " --> pdb=" O   ASP C 930 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASP C 935 " --> pdb=" O   GLN C 931 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 958 through 969
      removed outlier: 4.052A  pdb=" N   LEU C 962 " --> pdb=" O   GLY C 958 " (cutoff:3.500A)
      Proline residue:  C 964  - end of helix
    Processing helix  chain 'C' and resid 989 through 1003
      removed outlier: 3.916A  pdb=" N   LEU C 999 " --> pdb=" O   ALA C 995 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1024 through 1032
      removed outlier: 3.763A  pdb=" N   GLU C1030 " --> pdb=" O   THR C1026 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1033 through 1036
      removed outlier: 3.704A  pdb=" N   LYS C1036 " --> pdb=" O   GLU C1033 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1033 through 1036'
    Processing helix  chain 'C' and resid 1041 through 1048
    Processing helix  chain 'C' and resid 1049 through 1051
      No H-bonds generated for 'chain 'C' and resid 1049 through 1051'
    Processing helix  chain 'C' and resid 1066 through 1084
      removed outlier: 3.939A  pdb=" N   GLN C1073 " --> pdb=" O   LYS C1069 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE C1074 " --> pdb=" O   GLY C1070 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLU C1078 " --> pdb=" O   ILE C1074 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU C1079 " --> pdb=" O   ARG C1075 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS C1083 " --> pdb=" O   LEU C1079 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1103 through 1114
      removed outlier: 3.531A  pdb=" N   ALA C1109 " --> pdb=" O   ALA C1105 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU C1111 " --> pdb=" O   TYR C1107 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP C1112 " --> pdb=" O   MET C1108 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR C1113 " --> pdb=" O   ALA C1109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 704
      removed outlier: 3.753A  pdb=" N   HIS B 693 " --> pdb=" O   ALA B 689 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER B 699 " --> pdb=" O   ALA B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 727 through 733
      removed outlier: 3.870A  pdb=" N   VAL B 733 " --> pdb=" O   ILE B 729 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 756 through 761
      removed outlier: 3.685A  pdb=" N   LEU B 760 " --> pdb=" O   ASN B 756 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN B 761 " --> pdb=" O   PHE B 757 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 756 through 761'
    Processing helix  chain 'B' and resid 761 through 774
      removed outlier: 3.612A  pdb=" N   ARG B 766 " --> pdb=" O   SER B 762 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   TYR B 767 " --> pdb=" O   ASP B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 798
      removed outlier: 3.899A  pdb=" N   TYR B 794 " --> pdb=" O   GLN B 790 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   MET B 795 " --> pdb=" O   GLY B 791 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN B 797 " --> pdb=" O   GLN B 793 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 824
    Processing helix  chain 'B' and resid 825 through 836
    Processing helix  chain 'B' and resid 929 through 937
      removed outlier: 3.689A  pdb=" N   LEU B 934 " --> pdb=" O   ASP B 930 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ASP B 935 " --> pdb=" O   GLN B 931 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 958 through 969
      removed outlier: 4.052A  pdb=" N   LEU B 962 " --> pdb=" O   GLY B 958 " (cutoff:3.500A)
      Proline residue:  B 964  - end of helix
    Processing helix  chain 'B' and resid 989 through 1003
      removed outlier: 3.915A  pdb=" N   LEU B 999 " --> pdb=" O   ALA B 995 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1024 through 1032
      removed outlier: 3.764A  pdb=" N   GLU B1030 " --> pdb=" O   THR B1026 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1033 through 1036
      removed outlier: 3.703A  pdb=" N   LYS B1036 " --> pdb=" O   GLU B1033 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1033 through 1036'
    Processing helix  chain 'B' and resid 1041 through 1048
    Processing helix  chain 'B' and resid 1049 through 1051
      No H-bonds generated for 'chain 'B' and resid 1049 through 1051'
    Processing helix  chain 'B' and resid 1066 through 1084
      removed outlier: 3.939A  pdb=" N   GLN B1073 " --> pdb=" O   LYS B1069 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE B1074 " --> pdb=" O   GLY B1070 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLU B1078 " --> pdb=" O   ILE B1074 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU B1079 " --> pdb=" O   ARG B1075 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS B1083 " --> pdb=" O   LEU B1079 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1114
      removed outlier: 3.532A  pdb=" N   ALA B1109 " --> pdb=" O   ALA B1105 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU B1111 " --> pdb=" O   TYR B1107 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASP B1112 " --> pdb=" O   MET B1108 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR B1113 " --> pdb=" O   ALA B1109 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 778 through 785
      removed outlier: 6.134A  pdb=" N   LEU C 717 " --> pdb=" O   VAL C 810 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   GLY C 812 " --> pdb=" O   LEU C 717 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   MET C 719 " --> pdb=" O   GLY C 812 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ILE C1090 " --> pdb=" O   LEU C1122 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL C1124 " --> pdb=" O   ILE C1090 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   MET C1092 " --> pdb=" O   VAL C1124 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU C1089 " --> pdb=" O   THR C 947 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP C 949 " --> pdb=" O   LEU C1089 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   SER C1093 " --> pdb=" O   TRP C 951 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS C 977 " --> pdb=" O   GLY C 946 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 778 through 785
      removed outlier: 6.134A  pdb=" N   LEU C 717 " --> pdb=" O   VAL C 810 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   GLY C 812 " --> pdb=" O   LEU C 717 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   MET C 719 " --> pdb=" O   GLY C 812 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ILE C1090 " --> pdb=" O   LEU C1122 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL C1124 " --> pdb=" O   ILE C1090 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   MET C1092 " --> pdb=" O   VAL C1124 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU C1089 " --> pdb=" O   THR C 947 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP C 949 " --> pdb=" O   LEU C1089 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   SER C1093 " --> pdb=" O   TRP C 951 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLY C 983 " --> pdb=" O   TRP C 952 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   VAL C 980 " --> pdb=" O   THR C1011 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   LEU C1013 " --> pdb=" O   VAL C 980 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ILE C 982 " --> pdb=" O   LEU C1013 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 778 through 785
      removed outlier: 6.135A  pdb=" N   LEU B 717 " --> pdb=" O   VAL B 810 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   GLY B 812 " --> pdb=" O   LEU B 717 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   MET B 719 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ILE B1090 " --> pdb=" O   LEU B1122 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL B1124 " --> pdb=" O   ILE B1090 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   MET B1092 " --> pdb=" O   VAL B1124 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU B1089 " --> pdb=" O   THR B 947 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP B 949 " --> pdb=" O   LEU B1089 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER B1093 " --> pdb=" O   TRP B 951 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS B 977 " --> pdb=" O   GLY B 946 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 778 through 785
      removed outlier: 6.135A  pdb=" N   LEU B 717 " --> pdb=" O   VAL B 810 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   GLY B 812 " --> pdb=" O   LEU B 717 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   MET B 719 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ILE B1090 " --> pdb=" O   LEU B1122 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL B1124 " --> pdb=" O   ILE B1090 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   MET B1092 " --> pdb=" O   VAL B1124 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU B1089 " --> pdb=" O   THR B 947 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP B 949 " --> pdb=" O   LEU B1089 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER B1093 " --> pdb=" O   TRP B 951 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLY B 983 " --> pdb=" O   TRP B 952 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   VAL B 980 " --> pdb=" O   THR B1011 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   LEU B1013 " --> pdb=" O   VAL B 980 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ILE B 982 " --> pdb=" O   LEU B1013 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    714 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: 1.81

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1881
        1.34 -     1.45: 1057
        1.45 -     1.57: 3320
        1.57 -     1.69: 2
        1.69 -     1.81: 50
  Bond restraints: 6310
  Sorted by residual:
  bond pdb=" N   LEU C 933 "
       pdb=" CA  LEU C 933 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 9.97e+00
  bond pdb=" N   ILE C 709 "
       pdb=" CA  ILE C 709 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.83e+00
  bond pdb=" CB  THR C 792 "
       pdb=" CG2 THR C 792 "
    ideal  model  delta    sigma   weight residual
    1.521  1.425  0.096 3.30e-02 9.18e+02 8.52e+00
  bond pdb=" CB  THR B 792 "
       pdb=" CG2 THR B 792 "
    ideal  model  delta    sigma   weight residual
    1.521  1.425  0.096 3.30e-02 9.18e+02 8.40e+00
  bond pdb=" N   LYS C 710 "
       pdb=" CA  LYS C 710 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.87e+00
  ... (remaining 6305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 8326
        3.61 -     7.21: 175
        7.21 -    10.82: 16
       10.82 -    14.43: 6
       14.43 -    18.04: 1
  Bond angle restraints: 8524
  Sorted by residual:
  angle pdb=" CA  GLN B 941 "
        pdb=" CB  GLN B 941 "
        pdb=" CG  GLN B 941 "
      ideal   model   delta    sigma   weight residual
     114.10  127.34  -13.24 2.00e+00 2.50e-01 4.38e+01
  angle pdb=" CA  GLN C 941 "
        pdb=" CB  GLN C 941 "
        pdb=" CG  GLN C 941 "
      ideal   model   delta    sigma   weight residual
     114.10  127.29  -13.19 2.00e+00 2.50e-01 4.35e+01
  angle pdb=" N   LEU C 933 "
        pdb=" CA  LEU C 933 "
        pdb=" C   LEU C 933 "
      ideal   model   delta    sigma   weight residual
     111.14  117.95   -6.81 1.08e+00 8.57e-01 3.97e+01
  angle pdb=" CA  LEU B 933 "
        pdb=" CB  LEU B 933 "
        pdb=" CG  LEU B 933 "
      ideal   model   delta    sigma   weight residual
     116.30  134.34  -18.04 3.50e+00 8.16e-02 2.66e+01
  angle pdb=" CA  LEU C 933 "
        pdb=" C   LEU C 933 "
        pdb=" O   LEU C 933 "
      ideal   model   delta    sigma   weight residual
     120.70  115.84    4.86 1.03e+00 9.43e-01 2.22e+01
  ... (remaining 8519 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 3291
       17.54 -    35.08: 378
       35.08 -    52.62: 96
       52.62 -    70.16: 33
       70.16 -    87.70: 12
  Dihedral angle restraints: 3810
    sinusoidal: 1580
      harmonic: 2230
  Sorted by residual:
  dihedral pdb=" CA  GLN B 941 "
           pdb=" C   GLN B 941 "
           pdb=" N   LYS B 942 "
           pdb=" CA  LYS B 942 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.46   27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  GLN C 941 "
           pdb=" C   GLN C 941 "
           pdb=" N   LYS C 942 "
           pdb=" CA  LYS C 942 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.46   27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ALA B 735 "
           pdb=" C   ALA B 735 "
           pdb=" N   PHE B 736 "
           pdb=" CA  PHE B 736 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.27   21.73     0      5.00e+00 4.00e-02 1.89e+01
  ... (remaining 3807 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 730
       0.074 -    0.148: 193
       0.148 -    0.222: 22
       0.222 -    0.296: 3
       0.296 -    0.369: 2
  Chirality restraints: 950
  Sorted by residual:
  chirality pdb=" CG  LEU C1050 "
            pdb=" CB  LEU C1050 "
            pdb=" CD1 LEU C1050 "
            pdb=" CD2 LEU C1050 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.22   -0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" CG  LEU B1050 "
            pdb=" CB  LEU B1050 "
            pdb=" CD1 LEU B1050 "
            pdb=" CD2 LEU B1050 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.22   -0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" CA  ASP C 707 "
            pdb=" N   ASP C 707 "
            pdb=" C   ASP C 707 "
            pdb=" CB  ASP C 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 947 not shown)

  Planarity restraints: 1086
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 690 "    0.019 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   LEU C 690 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU C 690 "    0.024 2.00e-02 2.50e+03
        pdb=" N   THR C 691 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 690 "    0.019 2.00e-02 2.50e+03   3.76e-02 1.41e+01
        pdb=" C   LEU B 690 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   LEU B 690 "    0.024 2.00e-02 2.50e+03
        pdb=" N   THR B 691 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C1119 "    0.060 5.00e-02 4.00e+02   9.17e-02 1.34e+01
        pdb=" N   PRO C1120 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO C1120 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO C1120 "    0.051 5.00e-02 4.00e+02
  ... (remaining 1083 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1328
        2.78 -     3.31: 5451
        3.31 -     3.84: 9638
        3.84 -     4.37: 11199
        4.37 -     4.90: 19271
  Nonbonded interactions: 46887
  Sorted by model distance:
  nonbonded pdb=" CB  GLU B1030 "
            pdb=" OE2 GLU B1033 "
     model   vdw
     2.246 3.440
  nonbonded pdb=" CB  GLU C1030 "
            pdb=" OE2 GLU C1033 "
     model   vdw
     2.250 3.440
  nonbonded pdb=" O   VAL C 705 "
            pdb=" NH2 ARG B 769 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" OG  SER B1052 "
            pdb=" O   GLU B1054 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OG  SER C1052 "
            pdb=" O   GLU C1054 "
     model   vdw
     2.314 3.040
  ... (remaining 46882 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.130
  Find NCS groups from input model:        0.110
  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:2.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
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      :  0.008   0.096   6310  Z= 0.526
  Angle     :  1.244  18.035   8524  Z= 0.673
  Chirality :  0.067   0.369    950
  Planarity :  0.009   0.092   1086
  Dihedral  : 17.118  87.704   2366
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 12.95 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.64 (0.22), residues: 760
  helix: -3.93 (0.17), residues: 328
  sheet: -2.35 (0.45), residues: 134
  loop : -4.01 (0.24), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 973 
 HIS   0.009   0.002   HIS B 708 
 PHE   0.023   0.003   PHE C 736 
 TYR   0.018   0.003   TYR C 828 
 ARG   0.016   0.001   ARG C 753 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  710 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5813 (mtpt)
REVERT: C 1041 ASP cc_start: 0.5783 (m-30) cc_final: 0.4904 (m-30)
REVERT: C 1074 ILE cc_start: 0.7971 (mt) cc_final: 0.7675 (mt)
REVERT: B  729 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8684 (tt)
REVERT: B 1044 GLN cc_start: 0.7583 (pt0) cc_final: 0.6771 (tp40)
  outliers start: 42
  outliers final: 10
  residues processed: 194
  average time/residue: 0.2732
  time to fit residues: 63.9683
Evaluate side-chains
  119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  710 LYS
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue 1008 SER
Chi-restraints excluded: chain C residue 1093 SER
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  729 ILE
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue 1008 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
C 774 ASN
C 793 GLN
C 815 ASN
C 833 HIS
C1083 HIS
C1088 ASN
B 731 HIS
B 739 ASN
B 774 ASN
B 793 GLN
B 833 HIS
B1083 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.153879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.126642 restraints weight = 9027.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.128631 restraints weight = 6900.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.129835 restraints weight = 5752.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6310  Z= 0.237
  Angle     :  0.683  12.145   8524  Z= 0.349
  Chirality :  0.046   0.138    950
  Planarity :  0.006   0.080   1086
  Dihedral  :  6.865  41.750    854
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.15 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.59 (0.24), residues: 760
  helix: -2.64 (0.21), residues: 316
  sheet: -2.07 (0.44), residues: 144
  loop : -3.88 (0.24), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 770 
 HIS   0.005   0.001   HIS B1128 
 PHE   0.017   0.002   PHE B 736 
 TYR   0.015   0.002   TYR B1135 
 ARG   0.004   0.000   ARG C 803 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  933 LEU cc_start: 0.8307 (tp) cc_final: 0.8051 (tp)
REVERT: C  954 PHE cc_start: 0.5842 (t80) cc_final: 0.5468 (t80)
REVERT: B  730 LEU cc_start: 0.8690 (mp) cc_final: 0.8275 (tt)
REVERT: B  764 MET cc_start: 0.8130 (tpp) cc_final: 0.7863 (tpp)
REVERT: B  840 TYR cc_start: 0.8611 (m-80) cc_final: 0.8367 (m-80)
REVERT: B 1042 MET cc_start: 0.6814 (tpp) cc_final: 0.6498 (ttp)
  outliers start: 18
  outliers final: 14
  residues processed: 143
  average time/residue: 0.2176
  time to fit residues: 39.5237
Evaluate side-chains
  109 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  947 THR
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue 1065 LEU
Chi-restraints excluded: chain B residue 1086 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 55 optimal weight:    0.1980
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 58 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C 724 ASN
C1083 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.154378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.129830 restraints weight = 9127.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.130548 restraints weight = 8344.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131441 restraints weight = 6397.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6310  Z= 0.157
  Angle     :  0.618  10.021   8524  Z= 0.307
  Chirality :  0.045   0.216    950
  Planarity :  0.005   0.066   1086
  Dihedral  :  5.908  35.857    845
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.13 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.26), residues: 760
  helix: -1.70 (0.26), residues: 316
  sheet: -1.77 (0.44), residues: 144
  loop : -3.60 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 770 
 HIS   0.006   0.001   HIS B1128 
 PHE   0.013   0.001   PHE B 736 
 TYR   0.016   0.001   TYR B1135 
 ARG   0.003   0.000   ARG C 803 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  700 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7382 (mp)
REVERT: C  764 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7123 (tmm)
REVERT: C 1041 ASP cc_start: 0.6008 (m-30) cc_final: 0.5292 (m-30)
REVERT: B  700 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8558 (mm)
REVERT: B  730 LEU cc_start: 0.8572 (mp) cc_final: 0.8289 (tt)
REVERT: B  743 MET cc_start: 0.8645 (ttt) cc_final: 0.8315 (ttt)
  outliers start: 24
  outliers final: 15
  residues processed: 134
  average time/residue: 0.2162
  time to fit residues: 36.9419
Evaluate side-chains
  116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  700 LEU
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  982 ILE
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0050
   chunk 32 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0020
   overall best weight:    2.8008

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

Flipped N/Q/H residues before XYZ refinement:
C 734 HIS
C 739 ASN
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1077 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.145334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.119082 restraints weight = 9362.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.121231 restraints weight = 6784.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.122458 restraints weight = 5500.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6310  Z= 0.347
  Angle     :  0.746   8.944   8524  Z= 0.377
  Chirality :  0.049   0.204    950
  Planarity :  0.005   0.068   1086
  Dihedral  :  6.681  40.603    845
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 20.39 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.27), residues: 760
  helix: -1.53 (0.26), residues: 314
  sheet: -1.68 (0.44), residues: 144
  loop : -3.44 (0.29), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 973 
 HIS   0.007   0.002   HIS B1128 
 PHE   0.027   0.003   PHE C 954 
 TYR   0.013   0.002   TYR C1135 
 ARG   0.003   0.000   ARG C1038 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 106
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  700 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7838 (mm)
REVERT: C  764 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7242 (tmm)
REVERT: C  933 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8465 (mp)
REVERT: C  954 PHE cc_start: 0.6151 (t80) cc_final: 0.5938 (t80)
REVERT: B  700 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8657 (mm)
REVERT: B  821 ASP cc_start: 0.7546 (t70) cc_final: 0.7178 (t0)
REVERT: B  822 ILE cc_start: 0.9115 (tp) cc_final: 0.8907 (mt)
REVERT: B  826 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7358 (mm-30)
REVERT: B  977 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7195 (ptpp)
REVERT: B 1044 GLN cc_start: 0.7774 (pt0) cc_final: 0.7030 (tp40)
  outliers start: 41
  outliers final: 25
  residues processed: 141
  average time/residue: 0.2009
  time to fit residues: 36.6334
Evaluate side-chains
  125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  700 LEU
Chi-restraints excluded: chain C residue  739 ASN
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  933 LEU
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  982 ILE
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue 1074 ILE
Chi-restraints excluded: chain C residue 1093 SER
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  764 MET
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  947 THR
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue  960 THR
Chi-restraints excluded: chain B residue  977 LYS
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1065 LEU
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.149665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.123437 restraints weight = 9167.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.125572 restraints weight = 6759.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.127077 restraints weight = 5528.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6310  Z= 0.187
  Angle     :  0.635  13.684   8524  Z= 0.315
  Chirality :  0.045   0.200    950
  Planarity :  0.005   0.063   1086
  Dihedral  :  6.004  38.974    845
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 20.98 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.28), residues: 760
  helix: -1.02 (0.28), residues: 314
  sheet: -1.30 (0.48), residues: 130
  loop : -3.37 (0.28), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 770 
 HIS   0.009   0.001   HIS B1128 
 PHE   0.019   0.002   PHE C 954 
 TYR   0.015   0.001   TYR B1135 
 ARG   0.004   0.000   ARG B1075 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  764 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7056 (tmm)
REVERT: C  826 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7927 (mm-30)
REVERT: B  730 LEU cc_start: 0.8650 (mp) cc_final: 0.8323 (tt)
REVERT: B  743 MET cc_start: 0.8664 (ttt) cc_final: 0.8237 (ttp)
REVERT: B  821 ASP cc_start: 0.7636 (t70) cc_final: 0.7213 (t0)
REVERT: B  826 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7218 (mm-30)
REVERT: B 1007 PHE cc_start: 0.6981 (p90) cc_final: 0.6757 (p90)
REVERT: B 1044 GLN cc_start: 0.7463 (pt0) cc_final: 0.6902 (tp40)
REVERT: B 1061 ASN cc_start: 0.6750 (t0) cc_final: 0.5809 (p0)
  outliers start: 36
  outliers final: 24
  residues processed: 139
  average time/residue: 0.1943
  time to fit residues: 35.1212
Evaluate side-chains
  131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  739 ASN
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  771 LEU
Chi-restraints excluded: chain C residue  790 GLN
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  982 ILE
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  790 GLN
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue  960 THR
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1065 LEU
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Chi-restraints excluded: chain B residue 1131 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0670
   chunk 61 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
C 731 HIS
C 797 GLN
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 991 HIS
B1077 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.153014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.129599 restraints weight = 9198.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.131048 restraints weight = 7558.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131613 restraints weight = 6608.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.4728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6310  Z= 0.155
  Angle     :  0.604  11.971   8524  Z= 0.296
  Chirality :  0.044   0.177    950
  Planarity :  0.005   0.064   1086
  Dihedral  :  5.620  36.049    845
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.43 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.29), residues: 760
  helix: -0.48 (0.29), residues: 302
  sheet: -1.16 (0.48), residues: 130
  loop : -3.27 (0.28), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 770 
 HIS   0.009   0.001   HIS B1128 
 PHE   0.015   0.001   PHE B 736 
 TYR   0.014   0.001   TYR B1135 
 ARG   0.002   0.000   ARG B 848 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  700 LEU cc_start: 0.7758 (mm) cc_final: 0.7229 (mp)
REVERT: C  764 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.6922 (tmm)
REVERT: B  734 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7560 (t-90)
REVERT: B  743 MET cc_start: 0.8706 (ttt) cc_final: 0.8222 (ttp)
REVERT: B  826 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7312 (mm-30)
REVERT: B 1044 GLN cc_start: 0.7403 (pt0) cc_final: 0.6852 (tp40)
REVERT: B 1061 ASN cc_start: 0.6627 (t0) cc_final: 0.6016 (p0)
  outliers start: 29
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1943
  time to fit residues: 32.9887
Evaluate side-chains
  124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  771 LEU
Chi-restraints excluded: chain C residue  790 GLN
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  960 THR
Chi-restraints excluded: chain C residue  982 ILE
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  790 GLN
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue  960 THR
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Chi-restraints excluded: chain B residue 1131 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 67 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0670
   chunk 25 optimal weight:    0.0370
   chunk 53 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0370
   overall best weight:    0.3074

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

Flipped N/Q/H residues before XYZ refinement:
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.155544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.131166 restraints weight = 9071.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.132913 restraints weight = 6824.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.134332 restraints weight = 5688.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6310  Z= 0.134
  Angle     :  0.585  12.087   8524  Z= 0.287
  Chirality :  0.044   0.159    950
  Planarity :  0.004   0.062   1086
  Dihedral  :  5.274  35.116    845
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 22.17 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.29), residues: 760
  helix: -0.19 (0.30), residues: 302
  sheet: -1.01 (0.50), residues: 118
  loop : -3.10 (0.27), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 770 
 HIS   0.009   0.001   HIS B1128 
 PHE   0.030   0.001   PHE C 954 
 TYR   0.013   0.001   TYR B1135 
 ARG   0.005   0.000   ARG B 713 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  764 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6888 (tmm)
REVERT: C  933 LEU cc_start: 0.8555 (tp) cc_final: 0.8348 (mp)
REVERT: B  734 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7544 (t-90)
REVERT: B  743 MET cc_start: 0.8686 (ttt) cc_final: 0.8303 (ttp)
REVERT: B  974 LYS cc_start: 0.6820 (pttt) cc_final: 0.6459 (tptp)
REVERT: B 1044 GLN cc_start: 0.7346 (pt0) cc_final: 0.6880 (tp40)
REVERT: B 1061 ASN cc_start: 0.6453 (t0) cc_final: 0.5841 (p0)
  outliers start: 25
  outliers final: 16
  residues processed: 129
  average time/residue: 0.2106
  time to fit residues: 34.6994
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  790 GLN
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0970
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 48 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 739 ASN
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 991 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.151450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.129649 restraints weight = 9039.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.130191 restraints weight = 7723.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.130500 restraints weight = 6633.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.5094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6310  Z= 0.163
  Angle     :  0.619  10.995   8524  Z= 0.300
  Chirality :  0.044   0.160    950
  Planarity :  0.004   0.062   1086
  Dihedral  :  5.353  35.866    845
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.77 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.29), residues: 760
  helix: -0.12 (0.30), residues: 304
  sheet: -1.08 (0.46), residues: 130
  loop : -3.08 (0.29), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 770 
 HIS   0.005   0.001   HIS B1128 
 PHE   0.015   0.001   PHE B 736 
 TYR   0.011   0.001   TYR B1135 
 ARG   0.003   0.000   ARG B 713 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  764 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.6970 (tmm)
REVERT: C  933 LEU cc_start: 0.8573 (tp) cc_final: 0.8356 (mp)
REVERT: C  996 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.5479 (tpt)
REVERT: B  734 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7637 (t-90)
REVERT: B  743 MET cc_start: 0.8668 (ttt) cc_final: 0.8421 (ttt)
REVERT: B 1044 GLN cc_start: 0.7432 (pt0) cc_final: 0.6897 (tp40)
REVERT: B 1061 ASN cc_start: 0.6712 (t0) cc_final: 0.6169 (p0)
  outliers start: 27
  outliers final: 20
  residues processed: 120
  average time/residue: 0.1904
  time to fit residues: 29.9395
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  739 ASN
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  771 LEU
Chi-restraints excluded: chain C residue  790 GLN
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue  996 MET
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  764 MET
Chi-restraints excluded: chain B residue  790 GLN
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0010
   chunk 50 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
C 739 ASN
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.127355 restraints weight = 9057.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.128857 restraints weight = 7211.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.129950 restraints weight = 6156.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6310  Z= 0.199
  Angle     :  0.643  11.164   8524  Z= 0.314
  Chirality :  0.045   0.161    950
  Planarity :  0.004   0.061   1086
  Dihedral  :  5.548  37.532    845
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.92 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.29), residues: 760
  helix: -0.18 (0.30), residues: 304
  sheet: -1.16 (0.45), residues: 136
  loop : -3.22 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 770 
 HIS   0.006   0.001   HIS B1128 
 PHE   0.019   0.002   PHE B 736 
 TYR   0.011   0.002   TYR B1135 
 ARG   0.006   0.000   ARG B1075 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  764 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.6968 (tmm)
REVERT: C  933 LEU cc_start: 0.8559 (tp) cc_final: 0.8359 (mp)
REVERT: B  734 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7673 (t-90)
REVERT: B  743 MET cc_start: 0.8683 (ttt) cc_final: 0.8458 (ttt)
REVERT: B 1044 GLN cc_start: 0.7526 (pt0) cc_final: 0.7015 (tp40)
REVERT: B 1061 ASN cc_start: 0.6632 (t0) cc_final: 0.6058 (p0)
REVERT: B 1108 MET cc_start: 0.8319 (tpt) cc_final: 0.8030 (mmm)
  outliers start: 28
  outliers final: 24
  residues processed: 122
  average time/residue: 0.1880
  time to fit residues: 30.1506
Evaluate side-chains
  123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  717 LEU
Chi-restraints excluded: chain C residue  739 ASN
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  771 LEU
Chi-restraints excluded: chain C residue  790 GLN
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  982 ILE
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue  996 MET
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  764 MET
Chi-restraints excluded: chain B residue  790 GLN
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue  960 THR
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.149901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.126784 restraints weight = 9223.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.128431 restraints weight = 7114.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.129649 restraints weight = 5985.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.5255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6310  Z= 0.177
  Angle     :  0.635  11.209   8524  Z= 0.309
  Chirality :  0.045   0.157    950
  Planarity :  0.005   0.061   1086
  Dihedral  :  5.488  37.696    845
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 23.51 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.29), residues: 760
  helix: -0.05 (0.30), residues: 300
  sheet: -1.08 (0.46), residues: 134
  loop : -3.15 (0.29), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 770 
 HIS   0.006   0.001   HIS B1128 
 PHE   0.018   0.002   PHE B 736 
 TYR   0.011   0.001   TYR B1135 
 ARG   0.003   0.000   ARG B 713 

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  764 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7011 (tmm)
REVERT: C  933 LEU cc_start: 0.8582 (tp) cc_final: 0.8375 (mp)
REVERT: B  734 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7667 (t-90)
REVERT: B 1044 GLN cc_start: 0.7455 (pt0) cc_final: 0.6990 (tp40)
REVERT: B 1061 ASN cc_start: 0.6671 (t0) cc_final: 0.5971 (p0)
REVERT: B 1108 MET cc_start: 0.8291 (tpt) cc_final: 0.8008 (mmm)
  outliers start: 26
  outliers final: 24
  residues processed: 121
  average time/residue: 0.1870
  time to fit residues: 29.9169
Evaluate side-chains
  122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  748 VAL
Chi-restraints excluded: chain C residue  764 MET
Chi-restraints excluded: chain C residue  771 LEU
Chi-restraints excluded: chain C residue  790 GLN
Chi-restraints excluded: chain C residue  810 VAL
Chi-restraints excluded: chain C residue  927 ASN
Chi-restraints excluded: chain C residue  950 VAL
Chi-restraints excluded: chain C residue  960 THR
Chi-restraints excluded: chain C residue  982 ILE
Chi-restraints excluded: chain C residue  986 ILE
Chi-restraints excluded: chain C residue  996 MET
Chi-restraints excluded: chain C residue 1096 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  711 THR
Chi-restraints excluded: chain B residue  734 HIS
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  764 MET
Chi-restraints excluded: chain B residue  790 GLN
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  950 VAL
Chi-restraints excluded: chain B residue  960 THR
Chi-restraints excluded: chain B residue 1059 THR
Chi-restraints excluded: chain B residue 1086 THR
Chi-restraints excluded: chain B residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    0.0040
   chunk 59 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 72 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
C 739 ASN
** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.150327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.130039 restraints weight = 9275.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.130187 restraints weight = 7981.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.130203 restraints weight = 6919.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6310  Z= 0.166
  Angle     :  0.622  11.326   8524  Z= 0.302
  Chirality :  0.045   0.157    950
  Planarity :  0.005   0.061   1086
  Dihedral  :  5.390  37.663    845
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.66 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.30), residues: 760
  helix:  0.10 (0.31), residues: 294
  sheet: -1.06 (0.46), residues: 134
  loop : -3.02 (0.29), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 770 
 HIS   0.006   0.001   HIS B1128 
 PHE   0.017   0.001   PHE B 736 
 TYR   0.011   0.001   TYR B1135 
 ARG   0.003   0.000   ARG B 713 

===============================================================================
Job complete
usr+sys time: 2075.57 seconds
wall clock time: 38 minutes 3.31 seconds (2283.31 seconds total)