Starting phenix.real_space_refine
on Mon Jul 28 19:31:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6os9_20180/07_2025/6os9_20180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6os9_20180/07_2025/6os9_20180.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6os9_20180/07_2025/6os9_20180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6os9_20180/07_2025/6os9_20180.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6os9_20180/07_2025/6os9_20180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6os9_20180/07_2025/6os9_20180.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.011
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 2127 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      61      5.16       5
     C    5711      2.51       5
     N    1528      2.21       5
     O    1669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8969
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2415
          Classifications: {'peptide': 306}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "L"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 53
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1751
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2584
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 404
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1762
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 5.86, per 1000 atoms: 0.65
  Number of scatterers: 8969
  At special positions: 0
  Unit cell: (102.82, 121.9, 119.78, 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      61     16.00
     O    1669      8.00
     N    1528      7.00
     C    5711      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " 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: 2.34
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.2% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'R' and resid 51 through 55
      removed outlier: 3.607A  pdb=" N   LEU R  54 " --> pdb=" O   SER R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 91
    Processing helix  chain 'R' and resid 97 through 128
      removed outlier: 4.228A  pdb=" N   VAL R 101 " --> pdb=" O   LEU R  97 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
      removed outlier: 3.620A  pdb=" N   TYR R 125 " --> pdb=" O   PRO R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 172
      removed outlier: 3.514A  pdb=" N   GLY R 140 " --> pdb=" O   PHE R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 180
    Processing helix  chain 'R' and resid 181 through 199
    Processing helix  chain 'R' and resid 201 through 206
      removed outlier: 4.131A  pdb=" N   PHE R 205 " --> pdb=" O   VAL R 201 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 201 through 206'
    Processing helix  chain 'R' and resid 229 through 245
      removed outlier: 4.185A  pdb=" N   VAL R 235 " --> pdb=" O   ALA R 231 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 272
    Processing helix  chain 'R' and resid 295 through 329
      removed outlier: 3.568A  pdb=" N   ARG R 299 " --> pdb=" O   VAL R 295 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG R 306 " --> pdb=" O   VAL R 302 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 366
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 367 through 369
      No H-bonds generated for 'chain 'R' and resid 367 through 369'
    Processing helix  chain 'R' and resid 370 through 375
      removed outlier: 4.507A  pdb=" N   ILE R 374 " --> pdb=" O   ASN R 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.946A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.720A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.365A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.855A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.622A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 52 through 56
      removed outlier: 3.694A  pdb=" N   SER D  55 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLY D  56 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 52 through 56'
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.960A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.529A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.862A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.701A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.654A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.588A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.590A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 5.979A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.688A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.700A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.700A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130
      removed outlier: 3.702A  pdb=" N   ALA D 199 " --> pdb=" O   SER D 196 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136
      removed outlier: 6.692A  pdb=" N   LEU D 162 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   TYR D 178 " --> pdb=" O   LEU D 162 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TRP D 164 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1314 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: 2.47

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2828
        1.34 -     1.46: 2369
        1.46 -     1.59: 3873
        1.59 -     1.72: 0
        1.72 -     1.84: 90
  Bond restraints: 9160
  Sorted by residual:
  bond pdb=" C   MET R 120 "
       pdb=" N   PRO R 121 "
    ideal  model  delta    sigma   weight residual
    1.336  1.376 -0.041 1.23e-02 6.61e+03 1.09e+01
  bond pdb=" CG1 ILE B  80 "
       pdb=" CD1 ILE B  80 "
    ideal  model  delta    sigma   weight residual
    1.513  1.422  0.091 3.90e-02 6.57e+02 5.48e+00
  bond pdb=" CB  VAL R 159 "
       pdb=" CG1 VAL R 159 "
    ideal  model  delta    sigma   weight residual
    1.521  1.447  0.074 3.30e-02 9.18e+02 5.02e+00
  bond pdb=" CG  LEU B 146 "
       pdb=" CD1 LEU B 146 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.15e+00
  bond pdb=" CB  VAL R 313 "
       pdb=" CG2 VAL R 313 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 3.98e+00
  ... (remaining 9155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 12071
        2.73 -     5.46: 297
        5.46 -     8.20: 36
        8.20 -    10.93: 8
       10.93 -    13.66: 7
  Bond angle restraints: 12419
  Sorted by residual:
  angle pdb=" C   ARG D 179 "
        pdb=" N   MET D 180 "
        pdb=" CA  MET D 180 "
      ideal   model   delta    sigma   weight residual
     121.54  135.20  -13.66 1.91e+00 2.74e-01 5.11e+01
  angle pdb=" C   SER B 227 "
        pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
      ideal   model   delta    sigma   weight residual
     120.90  127.76   -6.86 1.41e+00 5.03e-01 2.37e+01
  angle pdb=" C   HIS B 142 "
        pdb=" N   THR B 143 "
        pdb=" CA  THR B 143 "
      ideal   model   delta    sigma   weight residual
     122.46  129.15   -6.69 1.41e+00 5.03e-01 2.25e+01
  angle pdb=" CA  ARG D 206 "
        pdb=" CB  ARG D 206 "
        pdb=" CG  ARG D 206 "
      ideal   model   delta    sigma   weight residual
     114.10  123.03   -8.93 2.00e+00 2.50e-01 1.99e+01
  angle pdb=" C   TYR D 178 "
        pdb=" N   ARG D 179 "
        pdb=" CA  ARG D 179 "
      ideal   model   delta    sigma   weight residual
     122.19  127.99   -5.80 1.41e+00 5.03e-01 1.69e+01
  ... (remaining 12414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 5128
       16.05 -    32.10: 236
       32.10 -    48.16: 42
       48.16 -    64.21: 4
       64.21 -    80.26: 7
  Dihedral angle restraints: 5417
    sinusoidal: 2069
      harmonic: 3348
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.26   80.26     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.73  -72.73     1      1.00e+01 1.00e-02 6.75e+01
  dihedral pdb=" CA  ASP B 290 "
           pdb=" C   ASP B 290 "
           pdb=" N   ASP B 291 "
           pdb=" CA  ASP B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.32   23.68     0      5.00e+00 4.00e-02 2.24e+01
  ... (remaining 5414 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1091
       0.068 -    0.136: 282
       0.136 -    0.204: 32
       0.204 -    0.272: 9
       0.272 -    0.340: 4
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CG  LEU D 162 "
            pdb=" CB  LEU D 162 "
            pdb=" CD1 LEU D 162 "
            pdb=" CD2 LEU D 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CB  VAL B  90 "
            pdb=" CA  VAL B  90 "
            pdb=" CG1 VAL B  90 "
            pdb=" CG2 VAL B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CB  ILE D 100 "
            pdb=" CA  ILE D 100 "
            pdb=" CG1 ILE D 100 "
            pdb=" CG2 ILE D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.49e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 142 "    0.026 2.00e-02 2.50e+03   2.67e-02 1.07e+01
        pdb=" CG  HIS B 142 "   -0.055 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 142 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 142 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 142 "   -0.006 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 142 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 111 "   -0.023 2.00e-02 2.50e+03   1.75e-02 7.67e+00
        pdb=" CG  TRP D 111 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 111 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 111 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 111 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 111 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 111 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 111 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 227 "   -0.006 2.00e-02 2.50e+03   1.71e-02 5.13e+00
        pdb=" CG  PHE D 227 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 227 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 227 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 227 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 227 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 227 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1880
        2.77 -     3.30: 7993
        3.30 -     3.84: 14878
        3.84 -     4.37: 17205
        4.37 -     4.90: 30523
  Nonbonded interactions: 72479
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR D 163 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ILE D 126 "
            pdb=" OG1 THR D 226 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.290 3.040
  ... (remaining 72474 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=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:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     23.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
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      :  0.010   0.091   9163  Z= 0.427
  Angle     :  1.084  13.659  12425  Z= 0.579
  Chirality :  0.062   0.340   1418
  Planarity :  0.006   0.051   1566
  Dihedral  : 10.142  77.253   3248
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.13 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.21), residues: 1132
  helix: -1.48 (0.20), residues: 391
  sheet: -1.61 (0.28), residues: 286
  loop : -2.01 (0.25), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.004   TRP D 111 
 HIS   0.028   0.004   HIS B 142 
 PHE   0.037   0.004   PHE A 199 
 TYR   0.036   0.004   TYR B 111 
 ARG   0.010   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17672 (  457)
  hydrogen bonds       : angle       7.33075 ( 1314)
  SS BOND              : bond        0.01086 (    3)
  SS BOND              : angle       2.77691 (    6)
  covalent geometry    : bond        0.01020 ( 9160)
  covalent geometry    : angle       1.08283 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 1.019 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  205 PHE cc_start: 0.7011 (p90) cc_final: 0.6554 (m-80)
REVERT: R  210 GLN cc_start: 0.8365 (tt0) cc_final: 0.8125 (tt0)
REVERT: R  232 THR cc_start: 0.7968 (m) cc_final: 0.7466 (m)
REVERT: R  325 MET cc_start: 0.8262 (ttm) cc_final: 0.8000 (ttm)
REVERT: A   49 ILE cc_start: 0.8426 (mt) cc_final: 0.8223 (OUTLIER)
REVERT: B   12 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8271 (tp30)
REVERT: B  170 ASP cc_start: 0.7912 (t70) cc_final: 0.7592 (t70)
REVERT: B  188 MET cc_start: 0.8426 (mmm) cc_final: 0.8158 (mmp)
REVERT: D   46 GLU cc_start: 0.8046 (tt0) cc_final: 0.7838 (tt0)
  outliers start: 2
  outliers final: 4
  residues processed: 225
  average time/residue: 1.2108
  time to fit residues: 291.0292
Evaluate side-chains
  152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain C residue   24 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 255 ASN
A 306 GLN
B  88 ASN
B  91 HIS
B 259 GLN
B 311 HIS
D 130 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.139357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.106138 restraints weight = 13281.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.52
r_work: 0.3437 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9163  Z= 0.142
  Angle     :  0.645   8.119  12425  Z= 0.339
  Chirality :  0.043   0.138   1418
  Planarity :  0.004   0.042   1566
  Dihedral  :  5.088  25.857   1252
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 13.31 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.23), residues: 1132
  helix:  0.46 (0.25), residues: 392
  sheet: -1.02 (0.28), residues: 292
  loop : -1.51 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 111 
 HIS   0.014   0.001   HIS B 142 
 PHE   0.012   0.002   PHE R 188 
 TYR   0.017   0.002   TYR A 296 
 ARG   0.011   0.001   ARG C  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (  457)
  hydrogen bonds       : angle       5.13682 ( 1314)
  SS BOND              : bond        0.00542 (    3)
  SS BOND              : angle       1.13063 (    6)
  covalent geometry    : bond        0.00307 ( 9160)
  covalent geometry    : angle       0.64420 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 1.062 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R  124 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8386 (mm)
REVERT: R  215 ASP cc_start: 0.7363 (t0) cc_final: 0.7133 (p0)
REVERT: A   24 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7255 (mtm110)
REVERT: A   49 ILE cc_start: 0.8212 (mt) cc_final: 0.7839 (mp)
REVERT: A   51 LYS cc_start: 0.8161 (tttt) cc_final: 0.7772 (mmtt)
REVERT: A   53 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6797 (mpt)
REVERT: A  298 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7338 (tm-30)
REVERT: B    8 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.7952 (mpt180)
REVERT: B   10 GLU cc_start: 0.7102 (tp30) cc_final: 0.6847 (tp30)
REVERT: B   12 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8456 (tm-30)
REVERT: B  226 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7867 (mp0)
REVERT: B  280 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8048 (tttp)
REVERT: B  294 CYS cc_start: 0.8635 (m) cc_final: 0.8366 (t)
REVERT: C   13 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8110 (ptp90)
REVERT: C   20 LYS cc_start: 0.8492 (ptmt) cc_final: 0.8111 (pttt)
REVERT: D   46 GLU cc_start: 0.8564 (tt0) cc_final: 0.8179 (tt0)
REVERT: D   76 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7982 (mptt)
  outliers start: 34
  outliers final: 10
  residues processed: 195
  average time/residue: 1.1400
  time to fit residues: 237.4943
Evaluate side-chains
  160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  116 LEU
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  186 LYS
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  311 ASN
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain D residue   76 LYS
Chi-restraints excluded: chain D residue   97 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 4 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 294 ASN
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.137701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.106384 restraints weight = 13401.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.45
r_work: 0.3415 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9163  Z= 0.157
  Angle     :  0.619   8.664  12425  Z= 0.322
  Chirality :  0.043   0.167   1418
  Planarity :  0.004   0.040   1566
  Dihedral  :  4.828  29.474   1252
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.48 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.25), residues: 1132
  helix:  1.16 (0.26), residues: 395
  sheet: -0.80 (0.29), residues: 293
  loop : -1.14 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 111 
 HIS   0.016   0.001   HIS B 142 
 PHE   0.021   0.002   PHE D  68 
 TYR   0.014   0.002   TYR A 296 
 ARG   0.008   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  457)
  hydrogen bonds       : angle       4.83302 ( 1314)
  SS BOND              : bond        0.00518 (    3)
  SS BOND              : angle       1.18834 (    6)
  covalent geometry    : bond        0.00365 ( 9160)
  covalent geometry    : angle       0.61863 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 1.008 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  102 HIS cc_start: 0.7748 (m90) cc_final: 0.7260 (m90)
REVERT: R  333 GLN cc_start: 0.8443 (mp10) cc_final: 0.8200 (pm20)
REVERT: A   51 LYS cc_start: 0.8309 (tttt) cc_final: 0.7834 (mmtt)
REVERT: A   53 MET cc_start: 0.7279 (mpt) cc_final: 0.6836 (mpt)
REVERT: A  205 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8072 (pmm150)
REVERT: B   12 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8505 (tm-30)
REVERT: B  217 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7570 (pmm)
REVERT: B  280 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7924 (tttp)
REVERT: C   13 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8063 (ptp90)
REVERT: C   20 LYS cc_start: 0.8470 (ptmt) cc_final: 0.8061 (pttt)
REVERT: D   46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8069 (tt0)
REVERT: D   76 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7957 (mptt)
  outliers start: 38
  outliers final: 12
  residues processed: 177
  average time/residue: 1.2445
  time to fit residues: 235.0223
Evaluate side-chains
  151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   76 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.139082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.107834 restraints weight = 13250.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.37
r_work: 0.3446 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9163  Z= 0.132
  Angle     :  0.602   8.283  12425  Z= 0.309
  Chirality :  0.042   0.144   1418
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.590  27.490   1252
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.23 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1132
  helix:  1.56 (0.26), residues: 394
  sheet: -0.70 (0.29), residues: 301
  loop : -0.94 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.013   0.001   HIS B 142 
 PHE   0.013   0.001   PHE D  68 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.009   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  457)
  hydrogen bonds       : angle       4.62205 ( 1314)
  SS BOND              : bond        0.00433 (    3)
  SS BOND              : angle       0.96020 (    6)
  covalent geometry    : bond        0.00301 ( 9160)
  covalent geometry    : angle       0.60164 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 1.048 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  102 HIS cc_start: 0.7695 (m90) cc_final: 0.7200 (m90)
REVERT: R  123 GLU cc_start: 0.7982 (tt0) cc_final: 0.7779 (tt0)
REVERT: R  188 PHE cc_start: 0.7596 (t80) cc_final: 0.7377 (t80)
REVERT: R  354 TYR cc_start: 0.7917 (m-10) cc_final: 0.7648 (m-10)
REVERT: A   51 LYS cc_start: 0.8130 (tttt) cc_final: 0.7642 (mmtt)
REVERT: A  205 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8067 (pmm-80)
REVERT: A  244 HIS cc_start: 0.8237 (t70) cc_final: 0.6950 (m90)
REVERT: B   12 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8500 (tm-30)
REVERT: B  226 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8021 (mp0)
REVERT: B  266 HIS cc_start: 0.8725 (t-90) cc_final: 0.8361 (t-90)
REVERT: B  280 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7847 (tttp)
REVERT: B  323 ASP cc_start: 0.8863 (t0) cc_final: 0.8625 (t0)
REVERT: C   13 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8012 (ptp90)
REVERT: C   20 LYS cc_start: 0.8396 (ptmt) cc_final: 0.7971 (pttt)
REVERT: C   48 ASP cc_start: 0.8482 (t0) cc_final: 0.8250 (t0)
REVERT: D   46 GLU cc_start: 0.8440 (tt0) cc_final: 0.8029 (tt0)
  outliers start: 34
  outliers final: 10
  residues processed: 176
  average time/residue: 1.1728
  time to fit residues: 220.7664
Evaluate side-chains
  156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain C residue   51 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0030
   chunk 45 optimal weight:    0.4980
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.136397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.103114 restraints weight = 13584.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.52
r_work: 0.3362 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9163  Z= 0.126
  Angle     :  0.605   9.985  12425  Z= 0.306
  Chirality :  0.043   0.243   1418
  Planarity :  0.003   0.043   1566
  Dihedral  :  4.403  27.274   1250
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.78 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1132
  helix:  1.68 (0.26), residues: 399
  sheet: -0.34 (0.30), residues: 297
  loop : -0.90 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.011   0.001   HIS B 142 
 PHE   0.015   0.001   PHE D  68 
 TYR   0.017   0.001   TYR A 296 
 ARG   0.010   0.000   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (  457)
  hydrogen bonds       : angle       4.47201 ( 1314)
  SS BOND              : bond        0.00403 (    3)
  SS BOND              : angle       0.92206 (    6)
  covalent geometry    : bond        0.00290 ( 9160)
  covalent geometry    : angle       0.60474 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.933 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  102 HIS cc_start: 0.7569 (m90) cc_final: 0.6911 (m90)
REVERT: R  123 GLU cc_start: 0.7910 (tt0) cc_final: 0.7577 (tt0)
REVERT: R  188 PHE cc_start: 0.7395 (t80) cc_final: 0.7120 (t80)
REVERT: R  333 GLN cc_start: 0.8520 (mp10) cc_final: 0.8285 (pm20)
REVERT: R  354 TYR cc_start: 0.7653 (m-10) cc_final: 0.7211 (m-10)
REVERT: A  205 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8075 (pmm-80)
REVERT: A  244 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.6888 (m90)
REVERT: A  253 ILE cc_start: 0.8674 (tp) cc_final: 0.8162 (pp)
REVERT: B  217 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7539 (pmm)
REVERT: B  226 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8287 (mt-10)
REVERT: B  280 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7696 (tttp)
REVERT: B  323 ASP cc_start: 0.8886 (t0) cc_final: 0.8606 (t0)
REVERT: C   14 LYS cc_start: 0.8249 (tmtp) cc_final: 0.7685 (mtmm)
REVERT: C   20 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7914 (pttt)
REVERT: D   46 GLU cc_start: 0.8505 (tt0) cc_final: 0.8038 (tt0)
  outliers start: 33
  outliers final: 12
  residues processed: 177
  average time/residue: 1.1158
  time to fit residues: 211.3390
Evaluate side-chains
  161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   51 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 3 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.136371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.102970 restraints weight = 13615.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.55
r_work: 0.3360 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9163  Z= 0.131
  Angle     :  0.611   8.685  12425  Z= 0.309
  Chirality :  0.042   0.158   1418
  Planarity :  0.003   0.050   1566
  Dihedral  :  4.359  27.772   1250
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.02 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1132
  helix:  1.83 (0.26), residues: 398
  sheet: -0.17 (0.30), residues: 297
  loop : -0.87 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.012   0.001   HIS B 142 
 PHE   0.013   0.001   PHE D  68 
 TYR   0.018   0.001   TYR A 296 
 ARG   0.011   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  457)
  hydrogen bonds       : angle       4.42567 ( 1314)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       0.98650 (    6)
  covalent geometry    : bond        0.00303 ( 9160)
  covalent geometry    : angle       0.61126 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 1.049 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R  102 HIS cc_start: 0.7702 (m90) cc_final: 0.7044 (m90)
REVERT: R  188 PHE cc_start: 0.7412 (t80) cc_final: 0.7119 (t80)
REVERT: R  210 GLN cc_start: 0.7674 (tt0) cc_final: 0.7123 (tt0)
REVERT: R  222 LEU cc_start: 0.7986 (mm) cc_final: 0.7697 (tp)
REVERT: A  205 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8125 (pmm-80)
REVERT: A  244 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.6818 (m90)
REVERT: A  253 ILE cc_start: 0.8676 (tp) cc_final: 0.8168 (pp)
REVERT: A  313 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7337 (ptp-170)
REVERT: B   13 GLN cc_start: 0.8647 (tp40) cc_final: 0.8411 (tp40)
REVERT: B  217 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7590 (pmm)
REVERT: B  226 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8248 (mt-10)
REVERT: B  280 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7667 (tttp)
REVERT: C   11 GLN cc_start: 0.6571 (pm20) cc_final: 0.6368 (pm20)
REVERT: C   13 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7943 (mtt180)
REVERT: C   14 LYS cc_start: 0.8247 (tmtp) cc_final: 0.7690 (mtmm)
REVERT: C   20 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7924 (pttt)
REVERT: C   48 ASP cc_start: 0.8550 (t0) cc_final: 0.8338 (t0)
REVERT: D   46 GLU cc_start: 0.8463 (tt0) cc_final: 0.7995 (tt0)
REVERT: D   76 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7910 (mptt)
  outliers start: 34
  outliers final: 17
  residues processed: 178
  average time/residue: 1.1537
  time to fit residues: 220.2856
Evaluate side-chains
  174 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  172 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0870
   chunk 45 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.137452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.104114 restraints weight = 13669.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.54
r_work: 0.3356 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9163  Z= 0.122
  Angle     :  0.621  10.683  12425  Z= 0.310
  Chirality :  0.042   0.124   1418
  Planarity :  0.004   0.053   1566
  Dihedral  :  4.252  26.254   1250
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.64 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1132
  helix:  1.95 (0.26), residues: 399
  sheet: -0.04 (0.31), residues: 295
  loop : -0.80 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 334 
 HIS   0.011   0.001   HIS B 142 
 PHE   0.012   0.001   PHE D  68 
 TYR   0.025   0.001   TYR A 296 
 ARG   0.013   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  457)
  hydrogen bonds       : angle       4.37697 ( 1314)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       0.87502 (    6)
  covalent geometry    : bond        0.00279 ( 9160)
  covalent geometry    : angle       0.62069 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.944 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R   86 PHE cc_start: 0.6577 (t80) cc_final: 0.6368 (t80)
REVERT: R  102 HIS cc_start: 0.7560 (m90) cc_final: 0.7001 (m90)
REVERT: R  188 PHE cc_start: 0.7395 (t80) cc_final: 0.7134 (t80)
REVERT: R  210 GLN cc_start: 0.7680 (tt0) cc_final: 0.7176 (tt0)
REVERT: A  205 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8130 (pmm-80)
REVERT: A  244 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.6855 (m90)
REVERT: A  253 ILE cc_start: 0.8731 (tp) cc_final: 0.8244 (pp)
REVERT: B  146 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8607 (mp)
REVERT: B  217 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7593 (pmm)
REVERT: B  226 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8301 (mt-10)
REVERT: B  280 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7650 (tttp)
REVERT: C   13 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7867 (mtt180)
REVERT: C   14 LYS cc_start: 0.8301 (tmtp) cc_final: 0.7726 (mtmm)
REVERT: C   20 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7892 (pttp)
REVERT: C   48 ASP cc_start: 0.8553 (t0) cc_final: 0.8321 (t0)
REVERT: D   46 GLU cc_start: 0.8413 (tt0) cc_final: 0.7934 (tt0)
  outliers start: 35
  outliers final: 22
  residues processed: 178
  average time/residue: 1.1463
  time to fit residues: 218.4581
Evaluate side-chains
  171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain R residue  357 SER
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  172 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 111 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0270
   chunk 54 optimal weight:    0.0010
   overall best weight:    1.0048

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

Flipped N/Q/H residues before XYZ refinement:
** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
A 306 GLN
A 331 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.136380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102843 restraints weight = 13851.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.56
r_work: 0.3359 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9163  Z= 0.142
  Angle     :  0.643  10.532  12425  Z= 0.323
  Chirality :  0.043   0.182   1418
  Planarity :  0.004   0.058   1566
  Dihedral  :  4.349  29.094   1250
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.05 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1132
  helix:  1.92 (0.26), residues: 400
  sheet:  0.05 (0.32), residues: 285
  loop : -0.79 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.012   0.001   HIS B 142 
 PHE   0.014   0.001   PHE D  68 
 TYR   0.034   0.001   TYR A 296 
 ARG   0.013   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  457)
  hydrogen bonds       : angle       4.39163 ( 1314)
  SS BOND              : bond        0.00432 (    3)
  SS BOND              : angle       0.99961 (    6)
  covalent geometry    : bond        0.00331 ( 9160)
  covalent geometry    : angle       0.64298 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 0.982 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R   86 PHE cc_start: 0.6621 (t80) cc_final: 0.6415 (t80)
REVERT: R  188 PHE cc_start: 0.7427 (t80) cc_final: 0.7127 (t80)
REVERT: R  210 GLN cc_start: 0.7671 (tt0) cc_final: 0.7083 (tt0)
REVERT: R  222 LEU cc_start: 0.7794 (mm) cc_final: 0.7433 (mt)
REVERT: R  243 MET cc_start: 0.9022 (tpp) cc_final: 0.8714 (tpp)
REVERT: A  205 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8121 (pmm-80)
REVERT: A  244 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.6801 (m90)
REVERT: B   13 GLN cc_start: 0.8666 (tp40) cc_final: 0.8443 (tp40)
REVERT: B  217 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7622 (pmm)
REVERT: B  226 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8249 (mt-10)
REVERT: B  266 HIS cc_start: 0.8692 (t-90) cc_final: 0.8279 (t-90)
REVERT: B  280 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7695 (tttp)
REVERT: B  323 ASP cc_start: 0.8920 (t0) cc_final: 0.8699 (t0)
REVERT: C   13 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7823 (mtt180)
REVERT: C   14 LYS cc_start: 0.8272 (tmtp) cc_final: 0.7712 (mtmm)
REVERT: C   20 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7901 (pttt)
REVERT: C   46 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8504 (mmpt)
REVERT: C   48 ASP cc_start: 0.8582 (t0) cc_final: 0.8335 (t0)
REVERT: D   46 GLU cc_start: 0.8406 (tt0) cc_final: 0.7925 (tt0)
  outliers start: 32
  outliers final: 22
  residues processed: 165
  average time/residue: 1.1564
  time to fit residues: 204.3826
Evaluate side-chains
  168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  172 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.133988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.100230 restraints weight = 13699.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.55
r_work: 0.3379 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9163  Z= 0.180
  Angle     :  0.677  10.429  12425  Z= 0.341
  Chirality :  0.044   0.179   1418
  Planarity :  0.004   0.064   1566
  Dihedral  :  4.522  32.397   1250
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.36 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1132
  helix:  1.83 (0.26), residues: 399
  sheet: -0.05 (0.32), residues: 292
  loop : -0.78 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.014   0.001   HIS B 142 
 PHE   0.017   0.002   PHE D  68 
 TYR   0.027   0.002   TYR A 296 
 ARG   0.013   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  457)
  hydrogen bonds       : angle       4.47195 ( 1314)
  SS BOND              : bond        0.00500 (    3)
  SS BOND              : angle       1.25693 (    6)
  covalent geometry    : bond        0.00426 ( 9160)
  covalent geometry    : angle       0.67665 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.963 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R  102 HIS cc_start: 0.7528 (m90) cc_final: 0.7245 (m90)
REVERT: R  188 PHE cc_start: 0.7534 (t80) cc_final: 0.7262 (t80)
REVERT: R  210 GLN cc_start: 0.7682 (tt0) cc_final: 0.7158 (tt0)
REVERT: R  222 LEU cc_start: 0.7835 (mm) cc_final: 0.7589 (mt)
REVERT: R  269 GLN cc_start: 0.7959 (pt0) cc_final: 0.7676 (pt0)
REVERT: A  244 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.6774 (m90)
REVERT: A  253 ILE cc_start: 0.8722 (tp) cc_final: 0.8282 (pp)
REVERT: B  142 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8393 (t-90)
REVERT: B  146 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8660 (mt)
REVERT: B  217 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7570 (pmm)
REVERT: B  226 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8281 (mt-10)
REVERT: B  266 HIS cc_start: 0.8651 (t-90) cc_final: 0.8219 (t-90)
REVERT: B  280 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7866 (tttp)
REVERT: B  323 ASP cc_start: 0.8912 (t0) cc_final: 0.8708 (t0)
REVERT: C   13 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7809 (mtt180)
REVERT: C   20 LYS cc_start: 0.8269 (ptmt) cc_final: 0.7891 (pttt)
REVERT: C   46 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8572 (mmpt)
REVERT: C   48 ASP cc_start: 0.8637 (t0) cc_final: 0.8398 (t0)
REVERT: D   11 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7175 (mp)
REVERT: D   46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8007 (tt0)
REVERT: D   76 LYS cc_start: 0.8661 (mtmm) cc_final: 0.7840 (pmtt)
  outliers start: 33
  outliers final: 19
  residues processed: 165
  average time/residue: 1.5929
  time to fit residues: 280.3417
Evaluate side-chains
  166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 3.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  172 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0020
   chunk 72 optimal weight:    0.0970
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.138271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.104963 restraints weight = 13700.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.57
r_work: 0.3457 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9163  Z= 0.123
  Angle     :  0.644  10.325  12425  Z= 0.325
  Chirality :  0.042   0.175   1418
  Planarity :  0.004   0.063   1566
  Dihedral  :  4.253  24.654   1250
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 22.91 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1132
  helix:  1.97 (0.26), residues: 398
  sheet:  0.05 (0.33), residues: 270
  loop : -0.72 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 316 
 HIS   0.010   0.001   HIS B 142 
 PHE   0.014   0.001   PHE R  74 
 TYR   0.039   0.001   TYR A 296 
 ARG   0.014   0.001   ARG D 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  457)
  hydrogen bonds       : angle       4.41624 ( 1314)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       0.86515 (    6)
  covalent geometry    : bond        0.00283 ( 9160)
  covalent geometry    : angle       0.64378 (12419)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 1.237 
Fit side-chains
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: R  188 PHE cc_start: 0.7390 (t80) cc_final: 0.7096 (t80)
REVERT: R  210 GLN cc_start: 0.7607 (tt0) cc_final: 0.7076 (tt0)
REVERT: R  222 LEU cc_start: 0.7723 (mm) cc_final: 0.7429 (mt)
REVERT: R  243 MET cc_start: 0.8971 (tpp) cc_final: 0.8721 (tpp)
REVERT: A  205 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7953 (pmm150)
REVERT: A  244 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.6724 (m90)
REVERT: A  253 ILE cc_start: 0.8649 (tp) cc_final: 0.8279 (pp)
REVERT: B  219 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7980 (ttm110)
REVERT: B  266 HIS cc_start: 0.8662 (t-90) cc_final: 0.8238 (t-90)
REVERT: C   13 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7793 (mtt180)
REVERT: C   14 LYS cc_start: 0.8067 (tptp) cc_final: 0.7630 (mtmm)
REVERT: C   20 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7854 (pttt)
REVERT: C   46 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8534 (mmpt)
REVERT: D   11 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7202 (mp)
REVERT: D   46 GLU cc_start: 0.8262 (tt0) cc_final: 0.7821 (tt0)
REVERT: D   76 LYS cc_start: 0.8586 (mtmm) cc_final: 0.7862 (pmtt)
  outliers start: 23
  outliers final: 18
  residues processed: 162
  average time/residue: 1.2966
  time to fit residues: 226.1099
Evaluate side-chains
  162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  225 THR
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  355 VAL
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  211 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0070
   chunk 8 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 108 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.9802

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.136911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.103395 restraints weight = 13697.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.57
r_work: 0.3436 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9163  Z= 0.143
  Angle     :  0.660  10.735  12425  Z= 0.332
  Chirality :  0.043   0.149   1418
  Planarity :  0.004   0.063   1566
  Dihedral  :  4.291  28.514   1250
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.63 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1132
  helix:  1.90 (0.26), residues: 399
  sheet:  0.08 (0.33), residues: 276
  loop : -0.65 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 316 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.016   0.001   PHE R  74 
 TYR   0.036   0.001   TYR A 296 
 ARG   0.014   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  457)
  hydrogen bonds       : angle       4.41641 ( 1314)
  SS BOND              : bond        0.00436 (    3)
  SS BOND              : angle       0.99799 (    6)
  covalent geometry    : bond        0.00335 ( 9160)
  covalent geometry    : angle       0.66026 (12419)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8057.58 seconds
wall clock time: 142 minutes 29.47 seconds (8549.47 seconds total)