Starting phenix.real_space_refine
on Wed Mar 12 10:46:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wcb_37437/03_2025/8wcb_37437_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wcb_37437/03_2025/8wcb_37437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wcb_37437/03_2025/8wcb_37437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wcb_37437/03_2025/8wcb_37437.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wcb_37437/03_2025/8wcb_37437_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wcb_37437/03_2025/8wcb_37437_neut.cif"
  }
  resolution = 3.1
  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=  -0.006 sd=   0.189
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4953      2.51       5
     N    1346      2.21       5
     O    1436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7784
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1686
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 5, 'TRANS': 214}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 133
          Unresolved non-hydrogen angles: 163
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 2354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2354
          Classifications: {'peptide': 323}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 317}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 161
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 3, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 93
    Chain: "R"
      Number of atoms: 1719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1719
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 76}
          Link IDs: {'PTRANS': 12, 'TRANS': 235}
          Chain breaks: 12
          Unresolved non-hydrogen bonds: 265
          Unresolved non-hydrogen angles: 333
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 29
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 7, 'GLU:plan': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 118
    Chain: "S"
      Number of atoms: 1681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1681
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 50
    Chain: "Y"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 337
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "R"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'HAI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.68, per 1000 atoms: 0.60
  Number of scatterers: 7784
  At special positions: 0
  Unit cell: (80.96, 118.68, 121.44, 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      49     16.00
     O    1436      8.00
     N    1346      7.00
     C    4953      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      32.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 4.033A  pdb=" N   ALA A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 265 through 277
      removed outlier: 3.575A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.886A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.387A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 4.037A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 335 through 347
      removed outlier: 4.229A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 392
      removed outlier: 3.619A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'R' and resid 24 through 46
      removed outlier: 4.317A  pdb=" N   ILE R  32 " --> pdb=" O   LEU R  28 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ILE R  33 " --> pdb=" O   MET R  29 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU R  34 " --> pdb=" O   SER R  30 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA R  35 " --> pdb=" O   LEU R  31 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL R  43 " --> pdb=" O   GLY R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 71
      removed outlier: 3.644A  pdb=" N   TRP R  59 " --> pdb=" O   THR R  55 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU R  60 " --> pdb=" O   PRO R  56 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU R  61 " --> pdb=" O   THR R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 83
      removed outlier: 3.539A  pdb=" N   CYS R  78 " --> pdb=" O   LEU R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 93
      No H-bonds generated for 'chain 'R' and resid 91 through 93'
    Processing helix  chain 'R' and resid 94 through 121
    Processing helix  chain 'R' and resid 135 through 157
      Proline residue:  R 150  - end of helix
    Processing helix  chain 'R' and resid 174 through 179
      removed outlier: 4.278A  pdb=" N   LEU R 178 " --> pdb=" O   GLN R 174 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY R 179 " --> pdb=" O   VAL R 175 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 174 through 179'
    Processing helix  chain 'R' and resid 186 through 194
      removed outlier: 3.755A  pdb=" N   VAL R 191 " --> pdb=" O   LYS R 187 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LEU R 192 " --> pdb=" O   VAL R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 220
      removed outlier: 3.762A  pdb=" N   ALA R 220 " --> pdb=" O   ALA R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 246 through 268
      removed outlier: 3.632A  pdb=" N   PHE R 257 " --> pdb=" O   MET R 253 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   CYS R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 279 through 284
    Processing helix  chain 'R' and resid 291 through 304
      Proline residue:  R 298  - end of helix
      removed outlier: 3.509A  pdb=" N   PHE R 303 " --> pdb=" O   MET R 299 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 309
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'Y' and resid 11 through 24
      removed outlier: 3.562A  pdb=" N   ASN Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 34
    Processing helix  chain 'Y' and resid 36 through 36
      No H-bonds generated for 'chain 'Y' and resid 36 through 36'
    Processing helix  chain 'Y' and resid 39 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.548A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.926A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 4.146A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 4.434A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.705A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 175 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191
      removed outlier: 3.996A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.589A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.686A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.437A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'S' and resid 174 through 176
    Processing sheet with id=AB4, first strand: chain 'S' and resid 189 through 190
    Processing sheet with id=AB5, first strand: chain 'S' and resid 225 through 227

    341 hydrogen bonds defined for protein.
    969 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: 2.09

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.15 -     1.50: 4776
        1.50 -     1.84: 3161
        1.84 -     2.19: 0
        2.19 -     2.53: 0
        2.53 -     2.87: 1
  Bond restraints: 7938
  Sorted by residual:
  bond pdb=" C   ALA B 309 "
       pdb=" N   HIS B 311 "
    ideal  model  delta    sigma   weight residual
    1.331  2.874 -1.543 1.33e-02 5.65e+03 1.35e+04
  bond pdb=" C   LEU R 286 "
       pdb=" N   TYR R 287 "
    ideal  model  delta    sigma   weight residual
    1.329  1.474 -0.145 1.40e-02 5.10e+03 1.07e+02
  bond pdb=" CA  ILE R 110 "
       pdb=" C   ILE R 110 "
    ideal  model  delta    sigma   weight residual
    1.524  1.445  0.079 1.18e-02 7.18e+03 4.48e+01
  bond pdb=" C   ILE S 189 "
       pdb=" O   ILE S 189 "
    ideal  model  delta    sigma   weight residual
    1.236  1.172  0.064 1.00e-02 1.00e+04 4.07e+01
  bond pdb=" C   THR R 101 "
       pdb=" O   THR R 101 "
    ideal  model  delta    sigma   weight residual
    1.237  1.163  0.073 1.16e-02 7.43e+03 3.98e+01
  ... (remaining 7933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.07: 10786
        9.07 -    18.13: 11
       18.13 -    27.20: 0
       27.20 -    36.27: 0
       36.27 -    45.33: 2
  Bond angle restraints: 10799
  Sorted by residual:
  angle pdb=" O   ALA B 309 "
        pdb=" C   ALA B 309 "
        pdb=" N   HIS B 311 "
      ideal   model   delta    sigma   weight residual
     122.89   81.76   41.13 1.22e+00 6.72e-01 1.14e+03
  angle pdb=" C   ALA B 309 "
        pdb=" N   HIS B 311 "
        pdb=" CA  HIS B 311 "
      ideal   model   delta    sigma   weight residual
     122.36  167.69  -45.33 1.60e+00 3.91e-01 8.03e+02
  angle pdb=" CA  ALA B 309 "
        pdb=" C   ALA B 309 "
        pdb=" N   HIS B 311 "
      ideal   model   delta    sigma   weight residual
     115.88  131.92  -16.04 1.28e+00 6.10e-01 1.57e+02
  angle pdb=" N   GLN R  52 "
        pdb=" CA  GLN R  52 "
        pdb=" C   GLN R  52 "
      ideal   model   delta    sigma   weight residual
     112.89  100.42   12.47 1.24e+00 6.50e-01 1.01e+02
  angle pdb=" N   LYS R  51 "
        pdb=" CA  LYS R  51 "
        pdb=" C   LYS R  51 "
      ideal   model   delta    sigma   weight residual
     114.39  100.50   13.89 1.45e+00 4.76e-01 9.18e+01
  ... (remaining 10794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.59: 4119
       14.59 -    29.18: 375
       29.18 -    43.77: 106
       43.77 -    58.36: 17
       58.36 -    72.96: 9
  Dihedral angle restraints: 4626
    sinusoidal: 1531
      harmonic: 3095
  Sorted by residual:
  dihedral pdb=" N   ASP R 102 "
           pdb=" C   ASP R 102 "
           pdb=" CA  ASP R 102 "
           pdb=" CB  ASP R 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.53  -14.73     0      2.50e+00 1.60e-01 3.47e+01
  dihedral pdb=" C   ASP R 102 "
           pdb=" N   ASP R 102 "
           pdb=" CA  ASP R 102 "
           pdb=" CB  ASP R 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.61   14.01     0      2.50e+00 1.60e-01 3.14e+01
  dihedral pdb=" C   SER R  48 "
           pdb=" N   SER R  48 "
           pdb=" CA  SER R  48 "
           pdb=" CB  SER R  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.77   12.17     0      2.50e+00 1.60e-01 2.37e+01
  ... (remaining 4623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 1200
       0.135 -    0.271: 40
       0.271 -    0.406: 14
       0.406 -    0.541: 2
       0.541 -    0.676: 1
  Chirality restraints: 1257
  Sorted by residual:
  chirality pdb=" CA  ASP R 102 "
            pdb=" N   ASP R 102 "
            pdb=" C   ASP R 102 "
            pdb=" CB  ASP R 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" CA  TYR S 235 "
            pdb=" N   TYR S 235 "
            pdb=" C   TYR S 235 "
            pdb=" CB  TYR S 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.72e+00
  chirality pdb=" CA  SER R  48 "
            pdb=" N   SER R  48 "
            pdb=" C   SER R  48 "
            pdb=" CB  SER R  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.36e+00
  ... (remaining 1254 not shown)

  Planarity restraints: 1372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 309 "    0.155 2.00e-02 2.50e+03   1.99e-01 3.95e+02
        pdb=" C   ALA B 309 "   -0.338 2.00e-02 2.50e+03
        pdb=" O   ALA B 309 "    0.128 2.00e-02 2.50e+03
        pdb=" N   HIS B 311 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 286 "    0.025 2.00e-02 2.50e+03   4.89e-02 2.39e+01
        pdb=" C   LEU R 286 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   LEU R 286 "    0.033 2.00e-02 2.50e+03
        pdb=" N   TYR R 287 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 279 "    0.064 5.00e-02 4.00e+02   9.81e-02 1.54e+01
        pdb=" N   PRO R 280 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO R 280 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO R 280 "    0.053 5.00e-02 4.00e+02
  ... (remaining 1369 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1702
        2.78 -     3.31: 7268
        3.31 -     3.84: 13051
        3.84 -     4.37: 15376
        4.37 -     4.90: 26617
  Nonbonded interactions: 64014
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" ND2 ASN A 387 "
            pdb=" O   ALA R 123 "
     model   vdw
     2.312 3.120
  ... (remaining 64009 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.290
  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:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6459
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      :  0.019   1.543   7938  Z= 0.859
  Angle     :  1.204  45.333  10799  Z= 0.800
  Chirality :  0.070   0.676   1257
  Planarity :  0.009   0.199   1372
  Dihedral  : 12.909  72.956   2608
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  1.64 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.40 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.27), residues: 1016
  helix:  0.04 (0.30), residues: 318
  sheet: -0.22 (0.34), residues: 244
  loop : -1.16 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 277 
 HIS   0.010   0.002   HIS A 357 
 PHE   0.021   0.002   PHE R 184 
 TYR   0.029   0.001   TYR R 301 
 ARG   0.007   0.000   ARG A 280 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.7677 (tptt) cc_final: 0.7443 (mmtt)
REVERT: R  276 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7276 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 147
  average time/residue: 0.1999
  time to fit residues: 39.1729
Evaluate side-chains
  119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  102 ASP
Chi-restraints excluded: chain R residue  109 SER
Chi-restraints excluded: chain R residue  276 TYR
Chi-restraints excluded: chain R residue  305 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
R  40 ASN
R 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.202653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.164575 restraints weight = 8552.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 2.11
r_work: 0.3882 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7938  Z= 0.208
  Angle     :  0.569   6.160  10799  Z= 0.303
  Chirality :  0.042   0.168   1257
  Planarity :  0.005   0.067   1372
  Dihedral  :  5.372  59.200   1142
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.19 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.27), residues: 1018
  helix:  1.20 (0.31), residues: 297
  sheet:  0.17 (0.33), residues: 246
  loop : -1.05 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 332 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.020   0.002   PHE R 184 
 TYR   0.011   0.001   TYR R 210 
 ARG   0.007   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.815 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.8114 (tptt) cc_final: 0.7878 (tptt)
REVERT: B  101 MET cc_start: 0.8436 (mtp) cc_final: 0.8185 (mtp)
REVERT: B  280 LYS cc_start: 0.7611 (mmpt) cc_final: 0.7360 (mmtt)
REVERT: R  276 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6513 (m-80)
  outliers start: 11
  outliers final: 5
  residues processed: 137
  average time/residue: 0.2038
  time to fit residues: 37.5157
Evaluate side-chains
  119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  276 TYR
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0050
   chunk 65 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 13 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B 259 GLN
R  62 HIS
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.197654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158302 restraints weight = 8664.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 2.17
r_work: 0.3819 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7938  Z= 0.227
  Angle     :  0.556   6.046  10799  Z= 0.294
  Chirality :  0.043   0.227   1257
  Planarity :  0.004   0.052   1372
  Dihedral  :  4.606  58.560   1137
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.19 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.27), residues: 1018
  helix:  1.52 (0.31), residues: 295
  sheet: -0.01 (0.33), residues: 253
  loop : -0.98 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 184 
 TYR   0.015   0.002   TYR B  85 
 ARG   0.008   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: R  276 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6550 (m-80)
  outliers start: 16
  outliers final: 8
  residues processed: 124
  average time/residue: 0.1950
  time to fit residues: 33.1531
Evaluate side-chains
  115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  276 TYR
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B 220 GLN
S 183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.194819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.154776 restraints weight = 8572.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 2.18
r_work: 0.3782 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7938  Z= 0.247
  Angle     :  0.564   6.821  10799  Z= 0.296
  Chirality :  0.043   0.199   1257
  Planarity :  0.004   0.046   1372
  Dihedral  :  4.665  56.737   1137
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.69 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.27), residues: 1018
  helix:  1.51 (0.31), residues: 295
  sheet: -0.17 (0.32), residues: 264
  loop : -0.83 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.014   0.002   PHE B 151 
 TYR   0.011   0.002   TYR S  50 
 ARG   0.006   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.988 
Fit side-chains
REVERT: B  105 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8103 (t80)
REVERT: B  311 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7050 (m-70)
REVERT: R  276 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6628 (m-80)
  outliers start: 20
  outliers final: 11
  residues processed: 132
  average time/residue: 0.2537
  time to fit residues: 46.8296
Evaluate side-chains
  124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  276 TYR
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 102 optimal weight:   10.0000
   chunk 29 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 259 GLN
S 183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.196523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.156907 restraints weight = 8579.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 2.16
r_work: 0.3805 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7938  Z= 0.202
  Angle     :  0.535   6.596  10799  Z= 0.283
  Chirality :  0.042   0.154   1257
  Planarity :  0.004   0.040   1372
  Dihedral  :  4.478  53.956   1137
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.55 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.27), residues: 1018
  helix:  1.77 (0.31), residues: 295
  sheet: -0.15 (0.32), residues: 264
  loop : -0.81 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 273 
 TYR   0.016   0.001   TYR B  85 
 ARG   0.007   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  232 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (ttp-110)
REVERT: B  197 ARG cc_start: 0.6809 (mmm160) cc_final: 0.6495 (mtp85)
REVERT: B  205 ASP cc_start: 0.7479 (t0) cc_final: 0.7272 (t0)
REVERT: B  332 TRP cc_start: 0.8386 (m-10) cc_final: 0.7732 (m-10)
REVERT: R   82 ARG cc_start: 0.7179 (ttp-170) cc_final: 0.6934 (ttp-170)
REVERT: R  276 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6596 (m-80)
  outliers start: 14
  outliers final: 7
  residues processed: 132
  average time/residue: 0.2023
  time to fit residues: 36.1210
Evaluate side-chains
  126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  276 TYR
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 79 optimal weight:    0.0770
   chunk 94 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6342

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
S 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.197095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.157697 restraints weight = 8579.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.17
r_work: 0.3816 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7938  Z= 0.191
  Angle     :  0.534   7.252  10799  Z= 0.281
  Chirality :  0.042   0.205   1257
  Planarity :  0.004   0.037   1372
  Dihedral  :  4.347  50.552   1137
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.92 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 1018
  helix:  1.84 (0.31), residues: 297
  sheet: -0.09 (0.33), residues: 256
  loop : -0.77 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 273 
 TYR   0.015   0.001   TYR B  85 
 ARG   0.008   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.868 
Fit side-chains
REVERT: B  197 ARG cc_start: 0.6732 (mmm160) cc_final: 0.6411 (mtp85)
REVERT: B  262 MET cc_start: 0.4380 (pmm) cc_final: 0.4125 (pmm)
REVERT: B  311 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.6976 (m-70)
REVERT: B  332 TRP cc_start: 0.8408 (m-10) cc_final: 0.7743 (m-10)
  outliers start: 16
  outliers final: 9
  residues processed: 127
  average time/residue: 0.1915
  time to fit residues: 33.4196
Evaluate side-chains
  122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 104 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0040
   chunk 94 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:    0.4980
   chunk 51 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
S 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.196480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.157126 restraints weight = 8632.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.18
r_work: 0.3807 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3669 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7938  Z= 0.192
  Angle     :  0.526   7.093  10799  Z= 0.277
  Chirality :  0.042   0.155   1257
  Planarity :  0.003   0.034   1372
  Dihedral  :  4.089  18.446   1135
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.63 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.92 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.27), residues: 1018
  helix:  1.81 (0.31), residues: 298
  sheet: -0.09 (0.33), residues: 256
  loop : -0.78 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 273 
 TYR   0.016   0.001   TYR B  85 
 ARG   0.006   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  280 ARG cc_start: 0.6732 (ttt-90) cc_final: 0.6248 (tpt90)
REVERT: B  197 ARG cc_start: 0.6718 (mmm160) cc_final: 0.6393 (mtp85)
REVERT: B  262 MET cc_start: 0.4377 (pmm) cc_final: 0.4110 (pmm)
REVERT: B  311 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6961 (m-70)
REVERT: B  332 TRP cc_start: 0.8383 (m-10) cc_final: 0.7705 (m-10)
REVERT: R   82 ARG cc_start: 0.6873 (ttp-170) cc_final: 0.6670 (ttp-170)
REVERT: S  219 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7579 (mp)
  outliers start: 17
  outliers final: 12
  residues processed: 126
  average time/residue: 0.2279
  time to fit residues: 38.4618
Evaluate side-chains
  125 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Chi-restraints excluded: chain S residue  219 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0060
   chunk 84 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
S 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.196704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.156962 restraints weight = 8715.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.22
r_work: 0.3806 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7938  Z= 0.195
  Angle     :  0.542  10.582  10799  Z= 0.281
  Chirality :  0.042   0.222   1257
  Planarity :  0.003   0.033   1372
  Dihedral  :  4.050  18.296   1135
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.34 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.87 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.27), residues: 1018
  helix:  1.84 (0.32), residues: 298
  sheet: -0.06 (0.33), residues: 256
  loop : -0.77 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.013   0.001   PHE A 376 
 TYR   0.017   0.001   TYR B  85 
 ARG   0.007   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: B  197 ARG cc_start: 0.6724 (mmm160) cc_final: 0.6415 (mtp85)
REVERT: B  262 MET cc_start: 0.4487 (pmm) cc_final: 0.4005 (pmm)
REVERT: B  311 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6970 (m-70)
REVERT: B  332 TRP cc_start: 0.8313 (m-10) cc_final: 0.7655 (m-10)
  outliers start: 16
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2360
  time to fit residues: 39.5706
Evaluate side-chains
  122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  253 MET
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 4 optimal weight:    0.0770
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0970
   chunk 8 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.198257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.159249 restraints weight = 8750.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.19
r_work: 0.3832 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7938  Z= 0.179
  Angle     :  0.534   9.996  10799  Z= 0.278
  Chirality :  0.042   0.191   1257
  Planarity :  0.003   0.032   1372
  Dihedral  :  3.962  18.316   1135
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.34 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.01 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 1018
  helix:  1.88 (0.31), residues: 305
  sheet: -0.03 (0.33), residues: 256
  loop : -0.77 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE A 376 
 TYR   0.016   0.001   TYR B  85 
 ARG   0.009   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 GLU cc_start: 0.6671 (mp0) cc_final: 0.6395 (mp0)
REVERT: B  197 ARG cc_start: 0.6699 (mmm160) cc_final: 0.6389 (mtp85)
REVERT: B  262 MET cc_start: 0.4473 (pmm) cc_final: 0.4048 (pmm)
REVERT: B  311 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.7031 (m-70)
REVERT: B  332 TRP cc_start: 0.8289 (m-10) cc_final: 0.7644 (m-10)
REVERT: S  219 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7691 (mp)
  outliers start: 16
  outliers final: 13
  residues processed: 126
  average time/residue: 0.2083
  time to fit residues: 35.3826
Evaluate side-chains
  126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Chi-restraints excluded: chain S residue  219 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 68 optimal weight:   20.0000
   chunk 56 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0970
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
R  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.196215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.156857 restraints weight = 8608.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.18
r_work: 0.3810 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3669 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7938  Z= 0.203
  Angle     :  0.541   7.587  10799  Z= 0.284
  Chirality :  0.043   0.191   1257
  Planarity :  0.003   0.037   1372
  Dihedral  :  4.036  18.230   1135
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.34 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.28 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.27), residues: 1018
  helix:  1.85 (0.31), residues: 305
  sheet: -0.08 (0.32), residues: 256
  loop : -0.75 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 376 
 TYR   0.018   0.001   TYR B  85 
 ARG   0.009   0.000   ARG A 280 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: B  197 ARG cc_start: 0.6720 (mmm160) cc_final: 0.6388 (mtp85)
REVERT: B  262 MET cc_start: 0.4545 (pmm) cc_final: 0.4099 (pmm)
REVERT: B  311 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7096 (m-70)
REVERT: B  332 TRP cc_start: 0.8388 (m-10) cc_final: 0.7735 (m-10)
REVERT: S  219 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7611 (mp)
  outliers start: 15
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2218
  time to fit residues: 37.1091
Evaluate side-chains
  124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ARG
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain S residue   98 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  206 SER
Chi-restraints excluded: chain S residue  219 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    0.2980
   chunk 77 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0670
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 86 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.4918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.198387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.159229 restraints weight = 8554.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.19
r_work: 0.3782 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6798
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7938  Z= 0.174
  Angle     :  0.537  10.633  10799  Z= 0.280
  Chirality :  0.042   0.189   1257
  Planarity :  0.003   0.041   1372
  Dihedral  :  3.939  18.317   1135
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.24 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.42 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.27), residues: 1018
  helix:  1.89 (0.31), residues: 305
  sheet: -0.03 (0.33), residues: 256
  loop : -0.74 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE A 376 
 TYR   0.016   0.001   TYR B  85 
 ARG   0.010   0.000   ARG A 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5161.27 seconds
wall clock time: 92 minutes 3.92 seconds (5523.92 seconds total)