Starting phenix.real_space_refine
on Wed Mar  4 13:28:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vgs_31978/03_2026/7vgs_31978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vgs_31978/03_2026/7vgs_31978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vgs_31978/03_2026/7vgs_31978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vgs_31978/03_2026/7vgs_31978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vgs_31978/03_2026/7vgs_31978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vgs_31978/03_2026/7vgs_31978.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.100
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5342 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6208      2.51       5
     N    1606      2.21       5
     O    1834      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9700
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1587
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 5, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 1683
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 218, 1657
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 17
      Conformer: "B"
        Number of residues, atoms: 218, 1657
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 17
          bond proxies already assigned to first conformer: 1662
    Chain: "D"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1580
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 4}
          Unresolved non-hydrogen planarities: 17
  Restraints were copied for chains:
    B, E, F
  Time building chain proxies: 2.68, per 1000 atoms: 0.28
  Number of scatterers: 9700
  At special positions: 0
  Unit cell: (73.455, 133.215, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1834      8.00
     N    1606      7.00
     C    6208      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG ACYS C 138 " - pdb=" SG ACYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG BCYS C 138 " - pdb=" SG BCYS C 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 140 " - pdb=" SG  CYS D 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  92 " distance=2.03
    Simple disulfide: pdb=" SG ACYS E 138 " - pdb=" SG ACYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG BCYS E 138 " - pdb=" SG BCYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 140 " - pdb=" SG  CYS F 195 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 572.8 milliseconds
  

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2360

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 20 sheets defined
      16.7% alpha, 32.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 37
      removed outlier: 3.631A  pdb=" N   LEU A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   PHE A  37 " --> pdb=" O   CYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 68
      removed outlier: 3.640A  pdb=" N   ILE A  49 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 78 through 106
      removed outlier: 3.991A  pdb=" N   ILE A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A  88 " --> pdb=" O   MET A  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 34
      removed outlier: 3.525A  pdb=" N   ASP C  34 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 132
      removed outlier: 3.682A  pdb=" N   GLY C 132 " --> pdb=" O   GLN C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 191
      removed outlier: 4.099A  pdb=" N   GLU C 191 " --> pdb=" O   LYS C 187 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 187 through 191'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.540A  pdb=" N   SER D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 37
      removed outlier: 4.426A  pdb=" N   PHE B  37 " --> pdb=" O   CYS B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 68
      removed outlier: 3.640A  pdb=" N   ILE B  49 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      Proline residue:  B  59  - end of helix
    Processing helix  chain 'B' and resid 78 through 106
      removed outlier: 3.992A  pdb=" N   ILE B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL B  88 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 34
      removed outlier: 3.525A  pdb=" N   ASP E  34 " --> pdb=" O   TYR E  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 125 through 132
      removed outlier: 3.682A  pdb=" N   GLY E 132 " --> pdb=" O   GLN E 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 187 through 191
      removed outlier: 4.099A  pdb=" N   GLU E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 187 through 191'
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.539A  pdb=" N   SER F  91 " --> pdb=" O   SER F  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132
      removed outlier: 3.902A  pdb=" N   ARG A 200 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LYS A 180 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   ARG A 198 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU A 149 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 13
      removed outlier: 6.405A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 109 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TRP C  39 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21
    Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122
      removed outlier: 5.101A  pdb=" N   SER C 135 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU C 185 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   VAL C 137 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU C 183 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   PHE C 139 " --> pdb=" O   SER C 181 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   SER C 181 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ASN C 141 " --> pdb=" O   MET C 179 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   MET C 179 " --> pdb=" O   ASN C 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159
      removed outlier: 4.205A  pdb=" N   TRP C 152 " --> pdb=" O   ARG C 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN C 149 " --> pdb=" O   THR C 201 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6
      removed outlier: 3.815A  pdb=" N   ALA D  79 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6
      removed outlier: 3.815A  pdb=" N   ALA D  79 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR D  78 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP D  73 " --> pdb=" O   THR D  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.719A  pdb=" N   TRP D  36 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER D  40 " --> pdb=" O   ASN D  44 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASN D  44 " --> pdb=" O   SER D  40 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124
      removed outlier: 6.309A  pdb=" N   TYR D 175 " --> pdb=" O   GLY D 144 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU D 174 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LEU D 170 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   THR D 176 " --> pdb=" O   ALA D 168 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ALA D 168 " --> pdb=" O   THR D 176 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   SER D 178 " --> pdb=" O   PHE D 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 151 through 154
    Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132
      removed outlier: 3.903A  pdb=" N   ARG B 200 " --> pdb=" O   TYR B 178 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LYS B 180 " --> pdb=" O   ARG B 198 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   ARG B 198 " --> pdb=" O   LYS B 180 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU B 149 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 13
      removed outlier: 6.406A  pdb=" N   LEU E  11 " --> pdb=" O   GLU E 109 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TRP E  39 " --> pdb=" O   LEU E  51 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 21
    Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 122
      removed outlier: 5.100A  pdb=" N   SER E 135 " --> pdb=" O   LEU E 185 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU E 185 " --> pdb=" O   SER E 135 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   VAL E 137 " --> pdb=" O   LEU E 183 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   LEU E 183 " --> pdb=" O   VAL E 137 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   PHE E 139 " --> pdb=" O   SER E 181 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   SER E 181 " --> pdb=" O   PHE E 139 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   ASN E 141 " --> pdb=" O   MET E 179 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   MET E 179 " --> pdb=" O   ASN E 141 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 159
      removed outlier: 4.204A  pdb=" N   TRP E 152 " --> pdb=" O   ARG E 159 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASN E 149 " --> pdb=" O   THR E 201 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6
      removed outlier: 3.815A  pdb=" N   ALA F  79 " --> pdb=" O   CYS F  22 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6
      removed outlier: 3.815A  pdb=" N   ALA F  79 " --> pdb=" O   CYS F  22 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR F  78 " --> pdb=" O   ASP F  73 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP F  73 " --> pdb=" O   THR F  78 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.720A  pdb=" N   TRP F  36 " --> pdb=" O   ILE F  48 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER F  40 " --> pdb=" O   ASN F  44 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASN F  44 " --> pdb=" O   SER F  40 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 120 through 124
      removed outlier: 6.308A  pdb=" N   TYR F 175 " --> pdb=" O   GLY F 144 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU F 174 " --> pdb=" O   LEU F 170 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LEU F 170 " --> pdb=" O   LEU F 174 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   THR F 176 " --> pdb=" O   ALA F 168 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ALA F 168 " --> pdb=" O   THR F 176 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   SER F 178 " --> pdb=" O   PHE F 166 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 151 through 154

    394 hydrogen bonds defined for protein.
    1018 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: 1.03

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3042
        1.35 -     1.46: 2479
        1.46 -     1.58: 4357
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 9952
  Sorted by residual:
  bond pdb=" CA  LYS A 162 "
       pdb=" CB  LYS A 162 "
    ideal  model  delta    sigma   weight residual
    1.522  1.553 -0.031 1.32e-02 5.74e+03 5.38e+00
  bond pdb=" CA  LYS B 162 "
       pdb=" CB  LYS B 162 "
    ideal  model  delta    sigma   weight residual
    1.522  1.553 -0.030 1.32e-02 5.74e+03 5.25e+00
  bond pdb=" CB  GLU A  18 "
       pdb=" CG  GLU A  18 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.94e+00
  bond pdb=" CB  GLU B  18 "
       pdb=" CG  GLU B  18 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.89e+00
  bond pdb=" C   ASP E  98 "
       pdb=" N   PRO E  99 "
    ideal  model  delta    sigma   weight residual
    1.333  1.347 -0.014 1.20e-02 6.94e+03 1.39e+00
  ... (remaining 9947 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 13250
        1.79 -     3.58: 288
        3.58 -     5.38: 31
        5.38 -     7.17: 18
        7.17 -     8.96: 5
  Bond angle restraints: 13592
  Sorted by residual:
  angle pdb=" CA  LEU A  90 "
        pdb=" CB  LEU A  90 "
        pdb=" CG  LEU A  90 "
      ideal   model   delta    sigma   weight residual
     116.30  125.26   -8.96 3.50e+00 8.16e-02 6.55e+00
  angle pdb=" CA  LEU B  90 "
        pdb=" CB  LEU B  90 "
        pdb=" CG  LEU B  90 "
      ideal   model   delta    sigma   weight residual
     116.30  125.23   -8.93 3.50e+00 8.16e-02 6.51e+00
  angle pdb=" N   PHE B  45 "
        pdb=" CA  PHE B  45 "
        pdb=" C   PHE B  45 "
      ideal   model   delta    sigma   weight residual
     113.61  109.94    3.67 1.50e+00 4.44e-01 6.00e+00
  angle pdb=" N   PHE A  45 "
        pdb=" CA  PHE A  45 "
        pdb=" C   PHE A  45 "
      ideal   model   delta    sigma   weight residual
     113.61  109.96    3.65 1.50e+00 4.44e-01 5.92e+00
  angle pdb=" N   SER C   7 "
        pdb=" CA  SER C   7 "
        pdb=" C   SER C   7 "
      ideal   model   delta    sigma   weight residual
     109.81  115.12   -5.31 2.21e+00 2.05e-01 5.78e+00
  ... (remaining 13587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 5490
       17.93 -    35.85: 368
       35.85 -    53.78: 44
       53.78 -    71.71: 10
       71.71 -    89.63: 8
  Dihedral angle restraints: 5920
    sinusoidal: 2228
      harmonic: 3692
  Sorted by residual:
  dihedral pdb=" CA  SER E   7 "
           pdb=" C   SER E   7 "
           pdb=" N   PRO E   8 "
           pdb=" CA  PRO E   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.11   28.89     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  SER C   7 "
           pdb=" C   SER C   7 "
           pdb=" N   PRO C   8 "
           pdb=" CA  PRO C   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.18   28.82     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CB  CYS D 140 "
           pdb=" SG  CYS D 140 "
           pdb=" SG  CYS D 195 "
           pdb=" CB  CYS D 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.01   39.99     1      1.00e+01 1.00e-02 2.24e+01
  ... (remaining 5917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1174
       0.044 -    0.087: 274
       0.087 -    0.131: 96
       0.131 -    0.175: 12
       0.175 -    0.218: 4
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CA  GLU A  18 "
            pdb=" N   GLU A  18 "
            pdb=" C   GLU A  18 "
            pdb=" CB  GLU A  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  GLU B  18 "
            pdb=" N   GLU B  18 "
            pdb=" C   GLU B  18 "
            pdb=" CB  GLU B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE C   2 "
            pdb=" CA  ILE C   2 "
            pdb=" CG1 ILE C   2 "
            pdb=" CG2 ILE C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1557 not shown)

  Planarity restraints: 1708
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 164 "   -0.037 5.00e-02 4.00e+02   5.56e-02 4.94e+00
        pdb=" N   PRO A 165 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 165 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 165 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 164 "    0.037 5.00e-02 4.00e+02   5.55e-02 4.93e+00
        pdb=" N   PRO B 165 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 165 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 165 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E   7 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO E   8 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO E   8 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E   8 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1705 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1405
        2.76 -     3.30: 9273
        3.30 -     3.83: 15939
        3.83 -     4.37: 18389
        4.37 -     4.90: 31637
  Nonbonded interactions: 76643
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 116 "
            pdb=" O   LEU A 133 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG1 THR B 116 "
            pdb=" O   LEU B 133 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ASN C  35 "
            pdb=" OG1 THR C  55 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   ASN E  35 "
            pdb=" OG1 THR E  55 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER D 190 "
            pdb=" OE1 GLU D 191 "
     model   vdw
     2.246 3.040
  ... (remaining 76638 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.27 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.810
  Find NCS groups from input model:        0.090
  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:6.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9962  Z= 0.129
  Angle     :  0.660   8.959  13612  Z= 0.342
  Chirality :  0.044   0.218   1560
  Planarity :  0.005   0.056   1708
  Dihedral  : 12.190  89.633   3530
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.56 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.24), residues: 1254
  helix: -0.43 (0.39), residues: 168
  sheet:  0.18 (0.25), residues: 490
  loop : -1.71 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 159 
 TYR   0.008   0.001   TYR C  53 
 PHE   0.008   0.001   PHE B  28 
 TRP   0.016   0.001   TRP B  92 
 HIS   0.002   0.001   HIS D  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9952)
  covalent geometry    : angle       0.65977 (13592)
  SS BOND              : bond        0.00258 (   10)
  SS BOND              : angle       0.51664 (   20)
  hydrogen bonds       : bond        0.14949 (  376)
  hydrogen bonds       : angle       6.68831 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.7120 (mmpt) cc_final: 0.6359 (pttt)
REVERT: A   31 TRP cc_start: 0.7726 (t-100) cc_final: 0.7226 (t60)
REVERT: A  127 THR cc_start: 0.7771 (p) cc_final: 0.7511 (t)
REVERT: A  164 LEU cc_start: 0.7705 (pt) cc_final: 0.7238 (pp)
REVERT: A  168 ILE cc_start: 0.8802 (mp) cc_final: 0.8574 (mp)
REVERT: C   40 TYR cc_start: 0.8653 (m-80) cc_final: 0.8440 (m-80)
REVERT: C  190 TYR cc_start: 0.7526 (t80) cc_final: 0.7289 (t80)
REVERT: C  191 GLU cc_start: 0.8183 (mp0) cc_final: 0.7827 (mp0)
REVERT: D   34 MET cc_start: 0.8571 (tpp) cc_final: 0.8356 (tpp)
REVERT: B  127 THR cc_start: 0.7956 (p) cc_final: 0.7662 (t)
REVERT: B  168 ILE cc_start: 0.8614 (mp) cc_final: 0.8399 (mp)
REVERT: E  159 ARG cc_start: 0.7322 (tpt-90) cc_final: 0.7087 (ttp80)
REVERT: E  191 GLU cc_start: 0.8096 (mp0) cc_final: 0.7597 (mp0)
REVERT: F   57 ASP cc_start: 0.7768 (m-30) cc_final: 0.7545 (m-30)
REVERT: F   82 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6846 (tm-30)
  outliers start: 0
  outliers final: 1
  residues processed: 300
  average time/residue: 0.4701
  time to fit residues: 152.2290
Evaluate side-chains
  188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  160 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.3980
   chunk 117 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 203 ASN
C  41 GLN
C  42 GLN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  39 GLN
E  41 GLN
E  42 GLN
F  35 ASN
F  39 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.144497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.099546 restraints weight = 64397.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 5.54
r_work: 0.3277 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3293
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3293
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9962  Z= 0.142
  Angle     :  0.670   8.917  13612  Z= 0.339
  Chirality :  0.044   0.170   1560
  Planarity :  0.005   0.055   1708
  Dihedral  :  4.715  31.497   1380
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.20 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.24), residues: 1254
  helix:  0.31 (0.39), residues: 184
  sheet:  0.26 (0.25), residues: 490
  loop : -1.70 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 215 
 TYR   0.018   0.001   TYR E  53 
 PHE   0.024   0.002   PHE A  45 
 TRP   0.015   0.002   TRP E 152 
 HIS   0.004   0.001   HIS E  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9952)
  covalent geometry    : angle       0.66995 (13592)
  SS BOND              : bond        0.00211 (   10)
  SS BOND              : angle       0.93697 (   20)
  hydrogen bonds       : bond        0.03529 (  376)
  hydrogen bonds       : angle       4.76510 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 196
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.7120 (mmpt) cc_final: 0.6322 (pttt)
REVERT: A   31 TRP cc_start: 0.7574 (t-100) cc_final: 0.7037 (t60)
REVERT: A   75 TRP cc_start: 0.5850 (m100) cc_final: 0.4825 (m-10)
REVERT: A  127 THR cc_start: 0.8260 (p) cc_final: 0.7861 (t)
REVERT: A  164 LEU cc_start: 0.8163 (pt) cc_final: 0.7659 (pp)
REVERT: A  168 ILE cc_start: 0.8706 (mp) cc_final: 0.8404 (mp)
REVERT: A  185 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7925 (tm-30)
REVERT: A  193 PHE cc_start: 0.7072 (t80) cc_final: 0.6204 (t80)
REVERT: C  159 ARG cc_start: 0.7014 (ttp80) cc_final: 0.6665 (tpt-90)
REVERT: C  190 TYR cc_start: 0.7159 (t80) cc_final: 0.6778 (t80)
REVERT: D   32 TYR cc_start: 0.8339 (m-10) cc_final: 0.8021 (m-10)
REVERT: D   81 MET cc_start: 0.7357 (ttt) cc_final: 0.6980 (ttm)
REVERT: D   82 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7395 (tm-30)
REVERT: D   89 GLU cc_start: 0.8502 (mp0) cc_final: 0.8105 (pp20)
REVERT: D   97 GLU cc_start: 0.8699 (pp20) cc_final: 0.8284 (pp20)
REVERT: B  127 THR cc_start: 0.8393 (p) cc_final: 0.8013 (t)
REVERT: B  168 ILE cc_start: 0.8701 (mp) cc_final: 0.8426 (mp)
REVERT: B  193 PHE cc_start: 0.6930 (t80) cc_final: 0.6499 (t80)
REVERT: E    3 VAL cc_start: 0.9078 (p) cc_final: 0.8877 (m)
REVERT: E  159 ARG cc_start: 0.7252 (tpt-90) cc_final: 0.7050 (tpt-90)
REVERT: E  191 GLU cc_start: 0.8085 (mp0) cc_final: 0.7713 (mp0)
REVERT: F   10 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8381 (tt0)
REVERT: F   32 TYR cc_start: 0.8366 (m-10) cc_final: 0.8067 (m-10)
REVERT: F   57 ASP cc_start: 0.8179 (m-30) cc_final: 0.7908 (m-30)
REVERT: F   80 TYR cc_start: 0.6710 (m-80) cc_final: 0.6168 (m-10)
REVERT: F   82 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7566 (tm-30)
REVERT: F   89 GLU cc_start: 0.8413 (mp0) cc_final: 0.8082 (pp20)
REVERT: F   97 GLU cc_start: 0.8508 (pp20) cc_final: 0.8146 (pp20)
  outliers start: 26
  outliers final: 14
  residues processed: 209
  average time/residue: 0.4775
  time to fit residues: 107.6921
Evaluate side-chains
  190 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue  169 ASP
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   71 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0980
   chunk 8 optimal weight:    3.9990
   chunk 102 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 86 optimal weight:    0.4980
   chunk 39 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.142744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.097384 restraints weight = 65911.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 5.56
r_work: 0.3245 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9962  Z= 0.125
  Angle     :  0.640   8.876  13612  Z= 0.322
  Chirality :  0.044   0.176   1560
  Planarity :  0.005   0.050   1708
  Dihedral  :  4.661  30.822   1378
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.77 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.24), residues: 1254
  helix:  0.33 (0.38), residues: 186
  sheet:  0.30 (0.25), residues: 490
  loop : -1.65 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  18 
 TYR   0.019   0.001   TYR E  53 
 PHE   0.015   0.001   PHE E 122 
 TRP   0.018   0.001   TRP E 152 
 HIS   0.003   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9952)
  covalent geometry    : angle       0.64062 (13592)
  SS BOND              : bond        0.00370 (   10)
  SS BOND              : angle       0.49693 (   20)
  hydrogen bonds       : bond        0.03396 (  376)
  hydrogen bonds       : angle       4.64236 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7530 (t-100) cc_final: 0.7040 (t60)
REVERT: A   87 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6071 (mp)
REVERT: A  127 THR cc_start: 0.8314 (p) cc_final: 0.7952 (t)
REVERT: A  135 GLU cc_start: 0.8101 (pm20) cc_final: 0.7808 (pm20)
REVERT: A  164 LEU cc_start: 0.8143 (pt) cc_final: 0.7570 (pp)
REVERT: A  166 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9140 (tttp)
REVERT: A  168 ILE cc_start: 0.8737 (mp) cc_final: 0.8412 (mp)
REVERT: A  185 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: A  193 PHE cc_start: 0.6961 (t80) cc_final: 0.6009 (t80)
REVERT: C  159 ARG cc_start: 0.7112 (ttp80) cc_final: 0.6805 (tpt-90)
REVERT: D   32 TYR cc_start: 0.8247 (m-10) cc_final: 0.7919 (m-10)
REVERT: D   82 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7288 (tm-30)
REVERT: D   89 GLU cc_start: 0.8509 (mp0) cc_final: 0.8166 (pp20)
REVERT: B   31 TRP cc_start: 0.7483 (t-100) cc_final: 0.7098 (t-100)
REVERT: B   45 PHE cc_start: 0.7378 (m-80) cc_final: 0.6776 (m-80)
REVERT: B  127 THR cc_start: 0.8450 (p) cc_final: 0.8089 (t)
REVERT: B  167 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8118 (pt0)
REVERT: B  168 ILE cc_start: 0.8726 (mp) cc_final: 0.8417 (mp)
REVERT: B  193 PHE cc_start: 0.6682 (t80) cc_final: 0.6458 (t80)
REVERT: E   36 TYR cc_start: 0.8640 (m-80) cc_final: 0.8418 (m-80)
REVERT: E  191 GLU cc_start: 0.8443 (mp0) cc_final: 0.8207 (mp0)
REVERT: F   10 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8499 (tt0)
REVERT: F   32 TYR cc_start: 0.8413 (m-10) cc_final: 0.8036 (m-10)
REVERT: F   57 ASP cc_start: 0.8214 (m-30) cc_final: 0.7982 (m-30)
REVERT: F   80 TYR cc_start: 0.7067 (m-80) cc_final: 0.6504 (m-80)
REVERT: F   81 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6812 (ttm)
REVERT: F   82 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7376 (tm-30)
REVERT: F   89 GLU cc_start: 0.8408 (mp0) cc_final: 0.8120 (pp20)
REVERT: F   97 GLU cc_start: 0.8704 (pp20) cc_final: 0.8285 (pp20)
  outliers start: 25
  outliers final: 15
  residues processed: 198
  average time/residue: 0.4528
  time to fit residues: 97.2168
Evaluate side-chains
  183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain C residue  169 ASP
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   81 MET
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 114 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0970
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
E  80 HIS
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 100 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.139249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.093961 restraints weight = 62704.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 5.32
r_work: 0.3186 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9962  Z= 0.141
  Angle     :  0.650   8.609  13612  Z= 0.329
  Chirality :  0.044   0.196   1560
  Planarity :  0.005   0.055   1708
  Dihedral  :  4.697  34.098   1378
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 19.49 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.24), residues: 1254
  helix:  0.43 (0.38), residues: 186
  sheet:  0.25 (0.25), residues: 492
  loop : -1.58 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  18 
 TYR   0.019   0.001   TYR E  53 
 PHE   0.021   0.002   PHE A  45 
 TRP   0.019   0.001   TRP E 152 
 HIS   0.002   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9952)
  covalent geometry    : angle       0.64993 (13592)
  SS BOND              : bond        0.00215 (   10)
  SS BOND              : angle       0.58727 (   20)
  hydrogen bonds       : bond        0.03414 (  376)
  hydrogen bonds       : angle       4.58425 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 175
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7511 (t-100) cc_final: 0.7044 (t60)
REVERT: A  127 THR cc_start: 0.8614 (p) cc_final: 0.8251 (t)
REVERT: A  135 GLU cc_start: 0.8224 (pm20) cc_final: 0.7970 (pm20)
REVERT: A  160 ASP cc_start: 0.7433 (m-30) cc_final: 0.7159 (t0)
REVERT: A  168 ILE cc_start: 0.8793 (mp) cc_final: 0.8467 (mp)
REVERT: C  158 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6904 (mt-10)
REVERT: C  159 ARG cc_start: 0.7135 (ttp80) cc_final: 0.6891 (tpt-90)
REVERT: C  171 ASP cc_start: 0.7811 (t0) cc_final: 0.7204 (t0)
REVERT: D   18 MET cc_start: 0.8677 (ptm) cc_final: 0.8397 (ptm)
REVERT: D   32 TYR cc_start: 0.8308 (m-10) cc_final: 0.8096 (m-10)
REVERT: D   80 TYR cc_start: 0.7384 (m-80) cc_final: 0.6878 (m-80)
REVERT: D   81 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7611 (ttt)
REVERT: D   82 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: D   89 GLU cc_start: 0.8631 (mp0) cc_final: 0.8218 (pp20)
REVERT: D   97 GLU cc_start: 0.8861 (pp20) cc_final: 0.8367 (pp20)
REVERT: B   31 TRP cc_start: 0.7495 (t-100) cc_final: 0.7101 (t-100)
REVERT: B   45 PHE cc_start: 0.7379 (m-80) cc_final: 0.6832 (m-80)
REVERT: B  127 THR cc_start: 0.8476 (p) cc_final: 0.8158 (t)
REVERT: B  167 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8237 (pt0)
REVERT: B  168 ILE cc_start: 0.8808 (mp) cc_final: 0.8501 (mp)
REVERT: E  171 ASP cc_start: 0.7726 (t0) cc_final: 0.7364 (t0)
REVERT: E  174 ASP cc_start: 0.7565 (p0) cc_final: 0.7112 (p0)
REVERT: F   10 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8339 (tt0)
REVERT: F   18 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8441 (ptm)
REVERT: F   32 TYR cc_start: 0.8286 (m-10) cc_final: 0.8051 (m-10)
REVERT: F   57 ASP cc_start: 0.8327 (m-30) cc_final: 0.8098 (m-30)
REVERT: F   80 TYR cc_start: 0.7407 (m-80) cc_final: 0.6837 (m-80)
REVERT: F   82 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: F   89 GLU cc_start: 0.8525 (mp0) cc_final: 0.8170 (pp20)
REVERT: F   97 GLU cc_start: 0.8801 (pp20) cc_final: 0.8330 (pp20)
  outliers start: 39
  outliers final: 20
  residues processed: 195
  average time/residue: 0.4646
  time to fit residues: 98.0582
Evaluate side-chains
  188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue   98 ASP
Chi-restraints excluded: chain C residue  169 ASP
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain E residue  175 SER
Chi-restraints excluded: chain E residue  216 ASN
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   18 MET
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 65 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   chunk 91 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 100 ASN
D 164 HIS
B 117 ASN
E  80 HIS
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.139724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.094579 restraints weight = 63600.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 5.31
r_work: 0.3196 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9962  Z= 0.120
  Angle     :  0.645   8.304  13612  Z= 0.321
  Chirality :  0.043   0.206   1560
  Planarity :  0.005   0.053   1708
  Dihedral  :  4.632  32.620   1378
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 21.85 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.25), residues: 1254
  helix:  0.48 (0.38), residues: 186
  sheet:  0.24 (0.25), residues: 492
  loop : -1.55 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  18 
 TYR   0.018   0.001   TYR E  53 
 PHE   0.013   0.001   PHE E 122 
 TRP   0.022   0.001   TRP A  58 
 HIS   0.002   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9952)
  covalent geometry    : angle       0.64482 (13592)
  SS BOND              : bond        0.00244 (   10)
  SS BOND              : angle       0.51942 (   20)
  hydrogen bonds       : bond        0.03298 (  376)
  hydrogen bonds       : angle       4.52854 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7461 (t-100) cc_final: 0.7030 (t60)
REVERT: A  127 THR cc_start: 0.8626 (p) cc_final: 0.8305 (t)
REVERT: A  160 ASP cc_start: 0.7396 (m-30) cc_final: 0.7159 (t0)
REVERT: A  168 ILE cc_start: 0.8770 (mp) cc_final: 0.8457 (mp)
REVERT: A  185 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8094 (tt0)
REVERT: C  171 ASP cc_start: 0.7830 (t0) cc_final: 0.7184 (t0)
REVERT: D   18 MET cc_start: 0.8635 (ptm) cc_final: 0.8323 (ptm)
REVERT: D   32 TYR cc_start: 0.8226 (m-10) cc_final: 0.7986 (m-10)
REVERT: D   80 TYR cc_start: 0.7370 (m-80) cc_final: 0.6856 (m-80)
REVERT: D   81 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7559 (ttt)
REVERT: D   82 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7377 (tm-30)
REVERT: D   89 GLU cc_start: 0.8634 (mp0) cc_final: 0.8213 (pp20)
REVERT: D   97 GLU cc_start: 0.8859 (pp20) cc_final: 0.8394 (pp20)
REVERT: D  208 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6438 (ttmt)
REVERT: B   15 LYS cc_start: 0.7019 (mmmm) cc_final: 0.6187 (pttt)
REVERT: B   31 TRP cc_start: 0.7467 (t-100) cc_final: 0.7116 (t-100)
REVERT: B   45 PHE cc_start: 0.7286 (m-80) cc_final: 0.6818 (m-80)
REVERT: B  127 THR cc_start: 0.8543 (p) cc_final: 0.8260 (t)
REVERT: B  167 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8230 (pt0)
REVERT: B  168 ILE cc_start: 0.8871 (mp) cc_final: 0.8577 (mp)
REVERT: E   36 TYR cc_start: 0.8631 (m-80) cc_final: 0.8421 (m-80)
REVERT: E  159 ARG cc_start: 0.7052 (tpt-90) cc_final: 0.6752 (tpt-90)
REVERT: E  171 ASP cc_start: 0.7821 (t0) cc_final: 0.7374 (t0)
REVERT: E  174 ASP cc_start: 0.7360 (p0) cc_final: 0.7070 (p0)
REVERT: E  215 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6232 (ttp-170)
REVERT: F   10 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8404 (tt0)
REVERT: F   32 TYR cc_start: 0.8253 (m-10) cc_final: 0.7999 (m-10)
REVERT: F   57 ASP cc_start: 0.8377 (m-30) cc_final: 0.8165 (m-30)
REVERT: F   80 TYR cc_start: 0.7403 (m-80) cc_final: 0.6851 (m-80)
REVERT: F   82 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: F   89 GLU cc_start: 0.8546 (mp0) cc_final: 0.8172 (pp20)
REVERT: F   97 GLU cc_start: 0.8793 (pp20) cc_final: 0.8269 (pp20)
  outliers start: 30
  outliers final: 15
  residues processed: 197
  average time/residue: 0.5092
  time to fit residues: 107.8446
Evaluate side-chains
  185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain D residue  208 LYS
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain E residue  215 ARG
Chi-restraints excluded: chain E residue  216 ASN
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   73 ASP
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0980
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
E  80 HIS
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.138745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.093313 restraints weight = 69651.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 5.52
r_work: 0.3167 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9962  Z= 0.126
  Angle     :  0.642   8.079  13612  Z= 0.323
  Chirality :  0.043   0.192   1560
  Planarity :  0.005   0.056   1708
  Dihedral  :  4.589  34.742   1378
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.10 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.66 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.25), residues: 1254
  helix:  0.57 (0.38), residues: 186
  sheet:  0.27 (0.25), residues: 492
  loop : -1.53 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E  18 
 TYR   0.018   0.001   TYR E  53 
 PHE   0.020   0.001   PHE A  45 
 TRP   0.023   0.001   TRP A  58 
 HIS   0.002   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9952)
  covalent geometry    : angle       0.64252 (13592)
  SS BOND              : bond        0.00177 (   10)
  SS BOND              : angle       0.49814 (   20)
  hydrogen bonds       : bond        0.03273 (  376)
  hydrogen bonds       : angle       4.48752 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7517 (t-100) cc_final: 0.7065 (t60)
REVERT: A  127 THR cc_start: 0.8573 (p) cc_final: 0.8244 (t)
REVERT: A  168 ILE cc_start: 0.8871 (mp) cc_final: 0.8560 (mp)
REVERT: C  158 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7034 (mt-10)
REVERT: C  171 ASP cc_start: 0.7758 (t0) cc_final: 0.7055 (t0)
REVERT: D   32 TYR cc_start: 0.8262 (m-10) cc_final: 0.8020 (m-10)
REVERT: D   80 TYR cc_start: 0.7433 (m-80) cc_final: 0.6888 (m-80)
REVERT: D   81 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7646 (ttt)
REVERT: D   82 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: D   89 GLU cc_start: 0.8694 (mp0) cc_final: 0.8461 (mt-10)
REVERT: D   97 GLU cc_start: 0.8900 (pp20) cc_final: 0.8408 (pp20)
REVERT: D  208 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6425 (ttmt)
REVERT: B   15 LYS cc_start: 0.6823 (mmmm) cc_final: 0.6118 (pttt)
REVERT: B   31 TRP cc_start: 0.7388 (t-100) cc_final: 0.7019 (t-100)
REVERT: B   45 PHE cc_start: 0.7285 (m-80) cc_final: 0.6825 (m-80)
REVERT: B  127 THR cc_start: 0.8504 (p) cc_final: 0.8215 (t)
REVERT: B  167 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8197 (pt0)
REVERT: B  168 ILE cc_start: 0.8900 (mp) cc_final: 0.8606 (mp)
REVERT: B  193 PHE cc_start: 0.7190 (t80) cc_final: 0.6831 (t80)
REVERT: E  158 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7145 (tp30)
REVERT: E  159 ARG cc_start: 0.6898 (tpt-90) cc_final: 0.6516 (tpt-90)
REVERT: E  171 ASP cc_start: 0.7871 (t0) cc_final: 0.7396 (t0)
REVERT: E  174 ASP cc_start: 0.7354 (p0) cc_final: 0.7071 (p0)
REVERT: F   10 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8411 (tt0)
REVERT: F   32 TYR cc_start: 0.8237 (m-10) cc_final: 0.7951 (m-10)
REVERT: F   80 TYR cc_start: 0.7497 (m-80) cc_final: 0.6978 (m-80)
REVERT: F   82 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7561 (tm-30)
REVERT: F   89 GLU cc_start: 0.8602 (mp0) cc_final: 0.8230 (pp20)
REVERT: F   97 GLU cc_start: 0.8811 (pp20) cc_final: 0.8325 (pp20)
  outliers start: 33
  outliers final: 21
  residues processed: 192
  average time/residue: 0.4848
  time to fit residues: 100.1833
Evaluate side-chains
  187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue  169 ASP
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain D residue  208 LYS
Chi-restraints excluded: chain D residue  210 ILE
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain E residue  216 ASN
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   73 ASP
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0670
   chunk 70 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 119 optimal weight:    3.9990
   overall best weight:    0.8920

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
E  80 HIS
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.137376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.091675 restraints weight = 77091.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 5.68
r_work: 0.3136 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9962  Z= 0.146
  Angle     :  0.666   9.711  13612  Z= 0.336
  Chirality :  0.044   0.204   1560
  Planarity :  0.005   0.055   1708
  Dihedral  :  4.669  34.158   1378
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.41 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.25), residues: 1254
  helix:  0.57 (0.38), residues: 186
  sheet:  0.20 (0.25), residues: 498
  loop : -1.54 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  18 
 TYR   0.020   0.001   TYR E  53 
 PHE   0.010   0.001   PHE C 213 
 TRP   0.023   0.001   TRP A  58 
 HIS   0.002   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9952)
  covalent geometry    : angle       0.66657 (13592)
  SS BOND              : bond        0.00244 (   10)
  SS BOND              : angle       0.54442 (   20)
  hydrogen bonds       : bond        0.03373 (  376)
  hydrogen bonds       : angle       4.51934 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7527 (t-100) cc_final: 0.7057 (t60)
REVERT: A  127 THR cc_start: 0.8552 (p) cc_final: 0.8215 (t)
REVERT: A  168 ILE cc_start: 0.8960 (mp) cc_final: 0.8671 (mp)
REVERT: C  158 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7149 (mt-10)
REVERT: D   32 TYR cc_start: 0.8346 (m-10) cc_final: 0.8111 (m-10)
REVERT: D   80 TYR cc_start: 0.7548 (m-80) cc_final: 0.6909 (m-80)
REVERT: D   81 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7868 (ttt)
REVERT: D   82 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: D   89 GLU cc_start: 0.8690 (mp0) cc_final: 0.8449 (mt-10)
REVERT: D   97 GLU cc_start: 0.8905 (pp20) cc_final: 0.8439 (pp20)
REVERT: D  208 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6409 (ttmt)
REVERT: B   15 LYS cc_start: 0.6777 (mmmm) cc_final: 0.6089 (pttt)
REVERT: B   31 TRP cc_start: 0.7376 (t-100) cc_final: 0.7016 (t-100)
REVERT: B   45 PHE cc_start: 0.7225 (m-80) cc_final: 0.6736 (m-80)
REVERT: B  127 THR cc_start: 0.8485 (p) cc_final: 0.8191 (t)
REVERT: B  167 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8191 (pt0)
REVERT: B  168 ILE cc_start: 0.8951 (mp) cc_final: 0.8700 (mp)
REVERT: E  159 ARG cc_start: 0.7208 (tpt-90) cc_final: 0.6847 (tpt-90)
REVERT: E  171 ASP cc_start: 0.7878 (t0) cc_final: 0.7423 (t0)
REVERT: E  174 ASP cc_start: 0.7486 (p0) cc_final: 0.7198 (p0)
REVERT: F   10 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8418 (mt-10)
REVERT: F   32 TYR cc_start: 0.8369 (m-10) cc_final: 0.8123 (m-10)
REVERT: F   82 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7542 (tm-30)
REVERT: F   89 GLU cc_start: 0.8668 (mp0) cc_final: 0.8280 (pp20)
REVERT: F   97 GLU cc_start: 0.8834 (pp20) cc_final: 0.8339 (pp20)
  outliers start: 34
  outliers final: 24
  residues processed: 186
  average time/residue: 0.4742
  time to fit residues: 95.3574
Evaluate side-chains
  185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue    4 MET
Chi-restraints excluded: chain C residue  169 ASP
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   13 LYS
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain D residue  208 LYS
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain E residue    4 MET
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  216 ASN
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0670
   chunk 51 optimal weight:    0.0970
   chunk 105 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0870
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0670
   chunk 84 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.1432

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  57 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
** E  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.140802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.096008 restraints weight = 67412.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 5.46
r_work: 0.3210 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9962  Z= 0.113
  Angle     :  0.648   9.666  13612  Z= 0.322
  Chirality :  0.043   0.195   1560
  Planarity :  0.005   0.054   1708
  Dihedral  :  4.490  34.625   1378
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 23.63 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.25), residues: 1254
  helix:  0.73 (0.38), residues: 184
  sheet:  0.39 (0.25), residues: 492
  loop : -1.55 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  18 
 TYR   0.014   0.001   TYR E  53 
 PHE   0.016   0.001   PHE E 213 
 TRP   0.018   0.001   TRP B  58 
 HIS   0.003   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9952)
  covalent geometry    : angle       0.64787 (13592)
  SS BOND              : bond        0.00169 (   10)
  SS BOND              : angle       0.49653 (   20)
  hydrogen bonds       : bond        0.03159 (  376)
  hydrogen bonds       : angle       4.44075 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7430 (t-100) cc_final: 0.6997 (t60)
REVERT: A  127 THR cc_start: 0.8479 (p) cc_final: 0.8177 (t)
REVERT: A  164 LEU cc_start: 0.8176 (pt) cc_final: 0.7482 (mm)
REVERT: A  168 ILE cc_start: 0.8758 (mp) cc_final: 0.8446 (mp)
REVERT: C   36 TYR cc_start: 0.8423 (m-80) cc_final: 0.8183 (m-80)
REVERT: C  158 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7024 (mt-10)
REVERT: C  159 ARG cc_start: 0.7195 (tpt-90) cc_final: 0.6917 (tpt-90)
REVERT: D   10 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8363 (tp30)
REVERT: D   32 TYR cc_start: 0.8213 (m-10) cc_final: 0.7948 (m-10)
REVERT: D   80 TYR cc_start: 0.7320 (m-80) cc_final: 0.6732 (m-80)
REVERT: D   82 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7430 (tm-30)
REVERT: D   87 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7422 (p)
REVERT: D   89 GLU cc_start: 0.8680 (mp0) cc_final: 0.8407 (mt-10)
REVERT: D   97 GLU cc_start: 0.8870 (pp20) cc_final: 0.8316 (pp20)
REVERT: B   15 LYS cc_start: 0.6657 (mmmm) cc_final: 0.6045 (pttt)
REVERT: B   31 TRP cc_start: 0.7372 (t-100) cc_final: 0.7087 (t-100)
REVERT: B   45 PHE cc_start: 0.7117 (m-80) cc_final: 0.6720 (m-80)
REVERT: B  127 THR cc_start: 0.8480 (p) cc_final: 0.8199 (t)
REVERT: B  135 GLU cc_start: 0.8012 (pm20) cc_final: 0.7621 (pm20)
REVERT: B  137 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7929 (mt-10)
REVERT: B  167 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8117 (pt0)
REVERT: B  168 ILE cc_start: 0.8857 (mp) cc_final: 0.8574 (mp)
REVERT: E   11 LEU cc_start: 0.8805 (tt) cc_final: 0.8473 (mp)
REVERT: E   36 TYR cc_start: 0.8599 (m-80) cc_final: 0.8313 (m-80)
REVERT: E  159 ARG cc_start: 0.7209 (tpt-90) cc_final: 0.6863 (tpt-90)
REVERT: E  171 ASP cc_start: 0.7806 (t0) cc_final: 0.7321 (t0)
REVERT: E  174 ASP cc_start: 0.7460 (p0) cc_final: 0.7227 (p0)
REVERT: F   10 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8331 (mt-10)
REVERT: F   32 TYR cc_start: 0.8231 (m-10) cc_final: 0.7887 (m-10)
REVERT: F   80 TYR cc_start: 0.7473 (m-80) cc_final: 0.6853 (m-80)
REVERT: F   82 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: F   89 GLU cc_start: 0.8645 (mp0) cc_final: 0.8289 (pp20)
REVERT: F   97 GLU cc_start: 0.8818 (pp20) cc_final: 0.8237 (pp20)
  outliers start: 20
  outliers final: 8
  residues processed: 185
  average time/residue: 0.4606
  time to fit residues: 92.1942
Evaluate side-chains
  171 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain E residue    4 MET
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 121 optimal weight:    7.9990
   chunk 114 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 89 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
E  80 HIS
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.136541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.090620 restraints weight = 75489.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 5.60
r_work: 0.3120 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9962  Z= 0.161
  Angle     :  0.676  10.886  13612  Z= 0.341
  Chirality :  0.044   0.208   1560
  Planarity :  0.005   0.057   1708
  Dihedral  :  4.705  35.145   1378
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.92 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.25), residues: 1254
  helix:  0.65 (0.37), residues: 188
  sheet:  0.21 (0.25), residues: 516
  loop : -1.57 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG E  18 
 TYR   0.020   0.002   TYR C  53 
 PHE   0.010   0.002   PHE B 112 
 TRP   0.026   0.001   TRP A  58 
 HIS   0.003   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9952)
  covalent geometry    : angle       0.67558 (13592)
  SS BOND              : bond        0.00321 (   10)
  SS BOND              : angle       0.61844 (   20)
  hydrogen bonds       : bond        0.03407 (  376)
  hydrogen bonds       : angle       4.53333 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7521 (t-100) cc_final: 0.7049 (t60)
REVERT: A   58 TRP cc_start: 0.7215 (m100) cc_final: 0.6952 (m100)
REVERT: A  127 THR cc_start: 0.8477 (p) cc_final: 0.8163 (t)
REVERT: A  168 ILE cc_start: 0.8943 (mp) cc_final: 0.8651 (mp)
REVERT: C  158 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7049 (mt-10)
REVERT: C  159 ARG cc_start: 0.7253 (tpt-90) cc_final: 0.6972 (tpt-90)
REVERT: D   32 TYR cc_start: 0.8411 (m-10) cc_final: 0.8190 (m-10)
REVERT: D   82 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: D   97 GLU cc_start: 0.8904 (pp20) cc_final: 0.8416 (pp20)
REVERT: B   15 LYS cc_start: 0.6560 (mmmm) cc_final: 0.5958 (pttt)
REVERT: B   31 TRP cc_start: 0.7371 (t-100) cc_final: 0.7022 (t-100)
REVERT: B   45 PHE cc_start: 0.7172 (m-80) cc_final: 0.6705 (m-80)
REVERT: B  127 THR cc_start: 0.8509 (p) cc_final: 0.8213 (t)
REVERT: B  167 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8223 (pt0)
REVERT: B  168 ILE cc_start: 0.8944 (mp) cc_final: 0.8696 (mp)
REVERT: E  159 ARG cc_start: 0.7202 (tpt-90) cc_final: 0.6870 (tpt-90)
REVERT: E  171 ASP cc_start: 0.7926 (t0) cc_final: 0.7491 (t0)
REVERT: E  174 ASP cc_start: 0.7540 (p0) cc_final: 0.7313 (p0)
REVERT: F   10 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8393 (mt-10)
REVERT: F   32 TYR cc_start: 0.8389 (m-10) cc_final: 0.8167 (m-10)
REVERT: F   82 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: F   89 GLU cc_start: 0.8682 (mp0) cc_final: 0.8321 (pp20)
REVERT: F   97 GLU cc_start: 0.8857 (pp20) cc_final: 0.8355 (pp20)
  outliers start: 22
  outliers final: 14
  residues processed: 176
  average time/residue: 0.4952
  time to fit residues: 93.8337
Evaluate side-chains
  174 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   13 LYS
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0870
   chunk 101 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 88 optimal weight:    0.5980
   chunk 118 optimal weight:    7.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
E  57 ASN
E  80 HIS
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.138290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092972 restraints weight = 70627.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 5.48
r_work: 0.3160 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9962  Z= 0.124
  Angle     :  0.676  11.945  13612  Z= 0.336
  Chirality :  0.044   0.209   1560
  Planarity :  0.005   0.055   1708
  Dihedral  :  4.633  36.161   1378
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.76 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.25), residues: 1254
  helix:  0.77 (0.38), residues: 188
  sheet:  0.38 (0.25), residues: 496
  loop : -1.54 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E  18 
 TYR   0.019   0.001   TYR E  53 
 PHE   0.016   0.001   PHE A  45 
 TRP   0.024   0.001   TRP A  58 
 HIS   0.003   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9952)
  covalent geometry    : angle       0.67627 (13592)
  SS BOND              : bond        0.00376 (   10)
  SS BOND              : angle       0.52536 (   20)
  hydrogen bonds       : bond        0.03260 (  376)
  hydrogen bonds       : angle       4.50962 ( 1018)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.7469 (t-100) cc_final: 0.7032 (t60)
REVERT: A  127 THR cc_start: 0.8491 (p) cc_final: 0.8170 (t)
REVERT: A  168 ILE cc_start: 0.8834 (mp) cc_final: 0.8548 (mp)
REVERT: C  158 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7055 (mt-10)
REVERT: C  159 ARG cc_start: 0.7299 (tpt-90) cc_final: 0.6988 (tpt-90)
REVERT: D   32 TYR cc_start: 0.8243 (m-10) cc_final: 0.7999 (m-10)
REVERT: D   80 TYR cc_start: 0.7701 (m-80) cc_final: 0.6943 (m-80)
REVERT: D   82 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7574 (tm-30)
REVERT: D   97 GLU cc_start: 0.8885 (pp20) cc_final: 0.8374 (pp20)
REVERT: B   15 LYS cc_start: 0.6545 (mmmm) cc_final: 0.5949 (pttt)
REVERT: B   31 TRP cc_start: 0.7358 (t-100) cc_final: 0.7024 (t-100)
REVERT: B   45 PHE cc_start: 0.7102 (m-80) cc_final: 0.6651 (m-80)
REVERT: B  127 THR cc_start: 0.8507 (p) cc_final: 0.8212 (t)
REVERT: B  167 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8199 (pt0)
REVERT: B  168 ILE cc_start: 0.8820 (mp) cc_final: 0.8582 (mp)
REVERT: E  159 ARG cc_start: 0.7055 (tpt-90) cc_final: 0.6674 (tpt-90)
REVERT: E  171 ASP cc_start: 0.7926 (t0) cc_final: 0.7482 (t0)
REVERT: E  174 ASP cc_start: 0.7508 (p0) cc_final: 0.7298 (p0)
REVERT: F   10 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8327 (mt-10)
REVERT: F   32 TYR cc_start: 0.8250 (m-10) cc_final: 0.7994 (m-10)
REVERT: F   82 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7566 (tm-30)
REVERT: F   89 GLU cc_start: 0.8672 (mp0) cc_final: 0.8307 (pp20)
REVERT: F   97 GLU cc_start: 0.8833 (pp20) cc_final: 0.8304 (pp20)
  outliers start: 15
  outliers final: 12
  residues processed: 168
  average time/residue: 0.5170
  time to fit residues: 93.5882
Evaluate side-chains
  171 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain D residue   10 GLU
Chi-restraints excluded: chain D residue   13 LYS
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  195 CYS
Chi-restraints excluded: chain B residue  167 GLU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain F residue   10 GLU
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue  195 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 80 optimal weight:    0.2980
   chunk 73 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 110 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 91 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
C  80 HIS
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.138223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092817 restraints weight = 71620.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 5.56
r_work: 0.3153 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9962  Z= 0.127
  Angle     :  0.673  11.748  13612  Z= 0.337
  Chirality :  0.044   0.239   1560
  Planarity :  0.005   0.055   1708
  Dihedral  :  4.584  34.739   1378
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 24.67 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.25), residues: 1254
  helix:  0.79 (0.38), residues: 188
  sheet:  0.38 (0.25), residues: 500
  loop : -1.52 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E  18 
 TYR   0.017   0.001   TYR E  53 
 PHE   0.020   0.001   PHE E 213 
 TRP   0.028   0.001   TRP B  58 
 HIS   0.003   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9952)
  covalent geometry    : angle       0.67345 (13592)
  SS BOND              : bond        0.00246 (   10)
  SS BOND              : angle       0.50379 (   20)
  hydrogen bonds       : bond        0.03270 (  376)
  hydrogen bonds       : angle       4.52348 ( 1018)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4215.61 seconds
wall clock time: 72 minutes 14.81 seconds (4334.81 seconds total)