Starting phenix.real_space_refine
on Thu Mar 13 14:20:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wwl_37892/03_2025/8wwl_37892.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wwl_37892/03_2025/8wwl_37892.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wwl_37892/03_2025/8wwl_37892.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wwl_37892/03_2025/8wwl_37892.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wwl_37892/03_2025/8wwl_37892.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wwl_37892/03_2025/8wwl_37892.cif"
  }
  resolution = 2.78
  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=   0.070
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      68      5.16       5
     C    5708      2.51       5
     N    1518      2.21       5
     O    1670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8964
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1749
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2239
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 15, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 32
    Chain: "L"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 139
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 5.67, per 1000 atoms: 0.63
  Number of scatterers: 8964
  At special positions: 0
  Unit cell: (87.74, 119.84, 120.91, 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      68     16.00
     O    1670      8.00
     N    1518      7.00
     C    5708      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 185 " - pdb=" SG  CYS R 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   7 " - pdb=" SG  CYS L  16 " 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: 2.41
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      38.3% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.596A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.590A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.044A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.763A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.635A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 4.522A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.502A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'R' and resid 108 through 137
      removed outlier: 3.638A  pdb=" N   MET R 112 " --> pdb=" O   ILE R 108 " (cutoff:3.500A)
      Proline residue:  R 113  - end of helix
    Processing helix  chain 'R' and resid 145 through 164
      removed outlier: 3.553A  pdb=" N   SER R 155 " --> pdb=" O   ILE R 151 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 164 through 174
      removed outlier: 3.605A  pdb=" N   MET R 168 " --> pdb=" O   GLY R 164 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   GLN R 171 " --> pdb=" O   PHE R 167 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU R 172 " --> pdb=" O   MET R 168 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   MET R 173 " --> pdb=" O   ILE R 169 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLY R 174 " --> pdb=" O   HIS R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 216
      removed outlier: 4.018A  pdb=" N   MET R 184 " --> pdb=" O   PHE R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 223
      removed outlier: 3.797A  pdb=" N   LYS R 222 " --> pdb=" O   SER R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 225 through 244
    Processing helix  chain 'R' and resid 244 through 250
      removed outlier: 3.583A  pdb=" N   TYR R 250 " --> pdb=" O   PRO R 246 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 286
      removed outlier: 3.720A  pdb=" N   LEU R 274 " --> pdb=" O   PRO R 270 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   TYR R 275 " --> pdb=" O   ASP R 271 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   TRP R 276 " --> pdb=" O   THR R 272 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE R 277 " --> pdb=" O   ASP R 273 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN R 281 " --> pdb=" O   PHE R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 303
    Processing helix  chain 'R' and resid 313 through 348
      Proline residue:  R 340  - end of helix
    Processing helix  chain 'R' and resid 355 through 384
      removed outlier: 4.089A  pdb=" N   SER R 373 " --> pdb=" O   GLY R 369 " (cutoff:3.500A)
      Proline residue:  R 377  - end of helix
      removed outlier: 3.542A  pdb=" N   CYS R 384 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 384 through 395
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.345A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.734A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.609A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.941A  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 105
      removed outlier: 6.140A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.720A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.941A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.402A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.748A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.880A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.257A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.209A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255
    Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9
      removed outlier: 3.537A  pdb=" N   VAL L  12 " --> pdb=" O   LEU L   9 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1302 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: 2.99

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2890
        1.34 -     1.46: 2196
        1.46 -     1.58: 3970
        1.58 -     1.70: 0
        1.70 -     1.81: 99
  Bond restraints: 9155
  Sorted by residual:
  bond pdb=" N   VAL E 147 "
       pdb=" CA  VAL E 147 "
    ideal  model  delta    sigma   weight residual
    1.454  1.461 -0.006 7.70e-03 1.69e+04 6.88e-01
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.57e-01
  bond pdb=" CA  GLY A 292 "
       pdb=" C   GLY A 292 "
    ideal  model  delta    sigma   weight residual
    1.521  1.513  0.008 1.13e-02 7.83e+03 4.84e-01
  bond pdb=" N   GLY A 292 "
       pdb=" CA  GLY A 292 "
    ideal  model  delta    sigma   weight residual
    1.443  1.449 -0.006 8.60e-03 1.35e+04 4.12e-01
  bond pdb=" C   VAL E  64 "
       pdb=" O   VAL E  64 "
    ideal  model  delta    sigma   weight residual
    1.232  1.240 -0.008 1.30e-02 5.92e+03 3.91e-01
  ... (remaining 9150 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 12083
        1.02 -     2.04: 281
        2.04 -     3.06: 37
        3.06 -     4.07: 13
        4.07 -     5.09: 10
  Bond angle restraints: 12424
  Sorted by residual:
  angle pdb=" C   ASP B 333 "
        pdb=" N   SER B 334 "
        pdb=" CA  SER B 334 "
      ideal   model   delta    sigma   weight residual
     122.74  125.82   -3.08 1.44e+00 4.82e-01 4.59e+00
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  125.25   -3.71 1.91e+00 2.74e-01 3.77e+00
  angle pdb=" CA  GLY A 292 "
        pdb=" C   GLY A 292 "
        pdb=" N   SER A 293 "
      ideal   model   delta    sigma   weight residual
     114.30  116.61   -2.31 1.20e+00 6.94e-01 3.69e+00
  angle pdb=" N   GLY B 330 "
        pdb=" CA  GLY B 330 "
        pdb=" C   GLY B 330 "
      ideal   model   delta    sigma   weight residual
     112.51  109.17    3.34 1.90e+00 2.77e-01 3.09e+00
  angle pdb=" C   ASP B 163 "
        pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
      ideal   model   delta    sigma   weight residual
     123.47  126.00   -2.53 1.53e+00 4.27e-01 2.74e+00
  ... (remaining 12419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.06: 5148
       14.06 -    28.12: 211
       28.12 -    42.18: 47
       42.18 -    56.24: 16
       56.24 -    70.30: 4
  Dihedral angle restraints: 5426
    sinusoidal: 2060
      harmonic: 3366
  Sorted by residual:
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.70   16.30     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.08   15.92     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.59   15.41     0      5.00e+00 4.00e-02 9.50e+00
  ... (remaining 5423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 857
       0.026 -    0.052: 345
       0.052 -    0.078: 126
       0.078 -    0.105: 65
       0.105 -    0.131: 32
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" CA  VAL E 199 "
            pdb=" N   VAL E 199 "
            pdb=" C   VAL E 199 "
            pdb=" CB  VAL E 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1422 not shown)

  Planarity restraints: 1571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.033 5.00e-02 4.00e+02   4.95e-02 3.91e+00
        pdb=" N   PRO B 236 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 106 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.54e+00
        pdb=" N   PRO E 107 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO E 107 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 107 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO B 194 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1568 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 188
        2.69 -     3.24: 8567
        3.24 -     3.79: 14268
        3.79 -     4.35: 20357
        4.35 -     4.90: 33380
  Nonbonded interactions: 76760
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 175 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" NH1 ARG B  96 "
            pdb=" OE2 GLU B 138 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   ALA R 364 "
            pdb=" OG  SER R 367 "
     model   vdw
     2.278 3.040
  ... (remaining 76755 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     24.850
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:14.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9155  Z= 0.144
  Angle     :  0.415   5.092  12424  Z= 0.227
  Chirality :  0.039   0.131   1425
  Planarity :  0.003   0.049   1571
  Dihedral  :  8.895  70.304   3242
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  3.41 %
    Favored  : 95.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.49 (0.25), residues: 1144
  helix:  0.53 (0.26), residues: 398
  sheet:  0.54 (0.30), residues: 291
  loop :  0.20 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.007   0.001   TYR E 103 
 ARG   0.002   0.000   ARG E  38 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 186
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8280 (mttt) cc_final: 0.8033 (mtpt)
REVERT: A   21 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7623 (mtm110)
REVERT: A   25 GLU cc_start: 0.7724 (tt0) cc_final: 0.7457 (tm-30)
REVERT: A   53 MET cc_start: 0.6223 (mtt) cc_final: 0.5954 (mtt)
REVERT: A  186 GLU cc_start: 0.7970 (tt0) cc_final: 0.7752 (mt-10)
REVERT: A  319 ILE cc_start: 0.8913 (mt) cc_final: 0.8704 (mm)
REVERT: A  349 LYS cc_start: 0.8292 (mttt) cc_final: 0.7789 (mtmt)
REVERT: B   96 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7318 (mtt-85)
REVERT: B  130 GLU cc_start: 0.7946 (mp0) cc_final: 0.7599 (mt-10)
REVERT: B  172 GLU cc_start: 0.7027 (tp30) cc_final: 0.6769 (tp30)
REVERT: B  188 MET cc_start: 0.8779 (mmm) cc_final: 0.8261 (mmm)
REVERT: B  189 SER cc_start: 0.8231 (p) cc_final: 0.7910 (t)
REVERT: E   83 MET cc_start: 0.8883 (mtm) cc_final: 0.8427 (mtp)
REVERT: E   85 SER cc_start: 0.8252 (m) cc_final: 0.7889 (t)
REVERT: E   90 ASP cc_start: 0.8183 (m-30) cc_final: 0.7978 (m-30)
REVERT: R  165 MET cc_start: 0.8508 (ttm) cc_final: 0.8292 (tmm)
REVERT: R  191 MET cc_start: 0.7686 (tpt) cc_final: 0.7238 (ttt)
REVERT: R  225 LYS cc_start: 0.8284 (mttt) cc_final: 0.8072 (mppt)
  outliers start: 8
  outliers final: 4
  residues processed: 191
  average time/residue: 1.3302
  time to fit residues: 269.7850
Evaluate side-chains
  146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 142
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0970
   chunk 88 optimal weight:    0.9980
   chunk 34 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 155 ASN
B 220 GLN
B 259 GLN
E 183 GLN
R 194 ASN
R 281 GLN
R 376 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.170577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.135166 restraints weight = 9474.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.63
r_work: 0.3298 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9155  Z= 0.231
  Angle     :  0.535   6.427  12424  Z= 0.292
  Chirality :  0.043   0.137   1425
  Planarity :  0.004   0.049   1571
  Dihedral  :  5.137  55.310   1259
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  9.40 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.02 (0.25), residues: 1144
  helix:  1.71 (0.26), residues: 395
  sheet:  0.32 (0.30), residues: 287
  loop :  0.13 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 179 
 PHE   0.016   0.002   PHE A 196 
 TYR   0.012   0.001   TYR R 341 
 ARG   0.007   0.001   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8304 (mttt) cc_final: 0.7962 (mtpt)
REVERT: A   21 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7506 (mtm110)
REVERT: A   25 GLU cc_start: 0.7949 (tt0) cc_final: 0.7566 (tt0)
REVERT: A   53 MET cc_start: 0.6098 (mtt) cc_final: 0.5771 (mtt)
REVERT: A  186 GLU cc_start: 0.8095 (tt0) cc_final: 0.7696 (mt-10)
REVERT: A  276 GLU cc_start: 0.7417 (mp0) cc_final: 0.7152 (mp0)
REVERT: A  349 LYS cc_start: 0.8101 (mttt) cc_final: 0.7637 (mtpt)
REVERT: B   96 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7623 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8126 (mp0) cc_final: 0.7651 (mt-10)
REVERT: B  146 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8319 (mp)
REVERT: B  188 MET cc_start: 0.8724 (mmm) cc_final: 0.8293 (mmm)
REVERT: B  189 SER cc_start: 0.8197 (p) cc_final: 0.7783 (t)
REVERT: B  217 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7026 (pp-130)
REVERT: B  219 ARG cc_start: 0.7431 (mmm160) cc_final: 0.6623 (mmt180)
REVERT: C   21 MET cc_start: 0.7768 (mmm) cc_final: 0.6916 (ttp)
REVERT: E   83 MET cc_start: 0.8850 (mtm) cc_final: 0.8365 (mtp)
REVERT: E  179 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7923 (tt0)
REVERT: R  169 ILE cc_start: 0.7557 (pt) cc_final: 0.6955 (mm)
REVERT: R  191 MET cc_start: 0.7676 (tpt) cc_final: 0.7062 (ttt)
REVERT: R  235 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8024 (mt)
REVERT: R  315 SER cc_start: 0.6641 (m) cc_final: 0.6226 (p)
  outliers start: 25
  outliers final: 11
  residues processed: 156
  average time/residue: 1.4726
  time to fit residues: 244.5124
Evaluate side-chains
  152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue  179 GLN
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  386 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 95 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 72 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 268 ASN
E 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.169639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134022 restraints weight = 9540.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.70
r_work: 0.3282 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9155  Z= 0.256
  Angle     :  0.525   6.227  12424  Z= 0.282
  Chirality :  0.043   0.138   1425
  Planarity :  0.004   0.051   1571
  Dihedral  :  4.825  54.398   1257
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.12 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.07 (0.25), residues: 1144
  helix:  2.03 (0.26), residues: 394
  sheet:  0.18 (0.30), residues: 287
  loop :  0.02 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.016   0.002   PHE A 196 
 TYR   0.011   0.001   TYR E 103 
 ARG   0.008   0.001   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8251 (mttt) cc_final: 0.7966 (mtpt)
REVERT: A   21 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7465 (mtm110)
REVERT: A   25 GLU cc_start: 0.7923 (tt0) cc_final: 0.7541 (tt0)
REVERT: A  186 GLU cc_start: 0.8074 (tt0) cc_final: 0.7674 (mt-10)
REVERT: A  276 GLU cc_start: 0.7232 (mp0) cc_final: 0.6933 (mp0)
REVERT: A  330 LYS cc_start: 0.7224 (mtmm) cc_final: 0.6027 (tttp)
REVERT: B   96 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7621 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8117 (mp0) cc_final: 0.7691 (mt-10)
REVERT: B  146 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8332 (mp)
REVERT: B  188 MET cc_start: 0.8730 (mmm) cc_final: 0.8379 (mmm)
REVERT: B  189 SER cc_start: 0.8189 (p) cc_final: 0.7778 (t)
REVERT: B  217 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7067 (pp-130)
REVERT: B  219 ARG cc_start: 0.7363 (mmm160) cc_final: 0.6646 (mmt180)
REVERT: C   21 MET cc_start: 0.7748 (mmm) cc_final: 0.6917 (ttp)
REVERT: E    6 GLU cc_start: 0.7452 (mp0) cc_final: 0.7124 (mt-10)
REVERT: E   83 MET cc_start: 0.8831 (mtm) cc_final: 0.8365 (mtp)
REVERT: E   93 MET cc_start: 0.8826 (ttt) cc_final: 0.8345 (tpp)
REVERT: E  179 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7978 (tt0)
REVERT: R  121 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7099 (mm)
REVERT: R  191 MET cc_start: 0.7645 (tpt) cc_final: 0.7049 (ttt)
REVERT: R  235 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8086 (mt)
REVERT: R  315 SER cc_start: 0.6739 (m) cc_final: 0.6287 (p)
  outliers start: 28
  outliers final: 14
  residues processed: 155
  average time/residue: 1.3592
  time to fit residues: 223.6273
Evaluate side-chains
  156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue  179 GLN
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  332 LEU
Chi-restraints excluded: chain R residue  386 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 87 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0170
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.172120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.136382 restraints weight = 9492.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.66
r_work: 0.3314 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9155  Z= 0.164
  Angle     :  0.469   6.477  12424  Z= 0.252
  Chirality :  0.041   0.137   1425
  Planarity :  0.004   0.051   1571
  Dihedral  :  4.643  59.984   1257
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.74 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.23 (0.25), residues: 1144
  helix:  2.34 (0.26), residues: 392
  sheet:  0.19 (0.30), residues: 284
  loop : -0.01 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A 196 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.008   0.000   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8266 (mttt) cc_final: 0.7982 (mtmt)
REVERT: A   21 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7496 (mtm110)
REVERT: A   25 GLU cc_start: 0.7946 (tt0) cc_final: 0.7539 (tm-30)
REVERT: A  186 GLU cc_start: 0.7954 (tt0) cc_final: 0.7647 (mt-10)
REVERT: A  209 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7556 (pttp)
REVERT: A  276 GLU cc_start: 0.7180 (mp0) cc_final: 0.6891 (mp0)
REVERT: A  308 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6890 (mt-10)
REVERT: A  330 LYS cc_start: 0.7258 (mtmm) cc_final: 0.5946 (tttp)
REVERT: A  349 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7515 (ttmt)
REVERT: B   96 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7582 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8072 (mp0) cc_final: 0.7673 (mt-10)
REVERT: B  188 MET cc_start: 0.8698 (mmm) cc_final: 0.8342 (mmm)
REVERT: B  189 SER cc_start: 0.8150 (p) cc_final: 0.7757 (t)
REVERT: B  274 THR cc_start: 0.8588 (p) cc_final: 0.8164 (p)
REVERT: C   21 MET cc_start: 0.7754 (mmm) cc_final: 0.6959 (ttp)
REVERT: E   83 MET cc_start: 0.8799 (mtm) cc_final: 0.8368 (mtp)
REVERT: E   93 MET cc_start: 0.8822 (ttt) cc_final: 0.8294 (tpp)
REVERT: E  179 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7851 (tt0)
REVERT: R  136 LYS cc_start: 0.7745 (ptpt) cc_final: 0.7351 (tptt)
REVERT: R  184 MET cc_start: 0.6991 (mmm) cc_final: 0.6675 (tpt)
REVERT: R  191 MET cc_start: 0.7426 (tpt) cc_final: 0.6864 (ttt)
REVERT: R  235 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8161 (mt)
REVERT: R  315 SER cc_start: 0.6527 (m) cc_final: 0.6107 (p)
  outliers start: 30
  outliers final: 15
  residues processed: 161
  average time/residue: 1.4350
  time to fit residues: 245.4564
Evaluate side-chains
  151 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue  179 GLN
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 91 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0370
   chunk 59 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0770
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.172965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.137485 restraints weight = 9526.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.61
r_work: 0.3341 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9155  Z= 0.145
  Angle     :  0.458   6.788  12424  Z= 0.244
  Chirality :  0.041   0.136   1425
  Planarity :  0.003   0.049   1571
  Dihedral  :  4.515  58.433   1257
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 10.54 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.33 (0.25), residues: 1144
  helix:  2.49 (0.26), residues: 395
  sheet:  0.26 (0.30), residues: 282
  loop : -0.05 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.009   0.000   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8221 (mttt) cc_final: 0.7948 (mtmt)
REVERT: A   21 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7568 (mtm110)
REVERT: A   25 GLU cc_start: 0.7954 (tt0) cc_final: 0.7536 (tm-30)
REVERT: A  186 GLU cc_start: 0.7939 (tt0) cc_final: 0.7645 (mt-10)
REVERT: A  209 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7498 (pttp)
REVERT: A  330 LYS cc_start: 0.7304 (mtmm) cc_final: 0.5973 (tttp)
REVERT: A  349 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7527 (ttmt)
REVERT: B   96 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7613 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8041 (mp0) cc_final: 0.7648 (tt0)
REVERT: B  188 MET cc_start: 0.8680 (mmm) cc_final: 0.8303 (mmm)
REVERT: B  189 SER cc_start: 0.8080 (p) cc_final: 0.7669 (t)
REVERT: B  274 THR cc_start: 0.8562 (p) cc_final: 0.8171 (p)
REVERT: C   21 MET cc_start: 0.7749 (mmm) cc_final: 0.6917 (ttp)
REVERT: E   83 MET cc_start: 0.8740 (mtm) cc_final: 0.8266 (mtp)
REVERT: E   93 MET cc_start: 0.8797 (ttt) cc_final: 0.8261 (tpp)
REVERT: R  136 LYS cc_start: 0.7769 (ptpt) cc_final: 0.7363 (tptt)
REVERT: R  184 MET cc_start: 0.7033 (mmm) cc_final: 0.6680 (tpt)
REVERT: R  191 MET cc_start: 0.7429 (tpt) cc_final: 0.6828 (ttt)
REVERT: R  235 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8184 (mt)
REVERT: R  332 LEU cc_start: 0.8120 (mt) cc_final: 0.7863 (tp)
  outliers start: 32
  outliers final: 15
  residues processed: 158
  average time/residue: 1.3291
  time to fit residues: 222.8637
Evaluate side-chains
  153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 4 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0870
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0980
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN
R 345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.172620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.137489 restraints weight = 9554.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.59
r_work: 0.3340 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9155  Z= 0.162
  Angle     :  0.465   7.037  12424  Z= 0.248
  Chirality :  0.041   0.137   1425
  Planarity :  0.003   0.048   1571
  Dihedral  :  4.516  57.616   1257
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 10.43 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.31 (0.25), residues: 1144
  helix:  2.51 (0.26), residues: 395
  sheet:  0.16 (0.30), residues: 287
  loop : -0.04 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.008   0.000   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8209 (mttt) cc_final: 0.7937 (mtmt)
REVERT: A   21 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7565 (mtm110)
REVERT: A   25 GLU cc_start: 0.7893 (tt0) cc_final: 0.7472 (tm-30)
REVERT: A  186 GLU cc_start: 0.7964 (tt0) cc_final: 0.7643 (mt-10)
REVERT: A  209 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7499 (pttp)
REVERT: A  276 GLU cc_start: 0.7165 (mp0) cc_final: 0.6899 (mp0)
REVERT: A  330 LYS cc_start: 0.7346 (mtmm) cc_final: 0.5979 (tttp)
REVERT: A  349 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7499 (ttmt)
REVERT: B   96 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7602 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8014 (mp0) cc_final: 0.7649 (tt0)
REVERT: B  137 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7336 (ttm-80)
REVERT: B  146 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8402 (mp)
REVERT: B  188 MET cc_start: 0.8674 (mmm) cc_final: 0.8299 (mmm)
REVERT: B  189 SER cc_start: 0.8114 (p) cc_final: 0.7701 (t)
REVERT: B  274 THR cc_start: 0.8607 (p) cc_final: 0.8260 (p)
REVERT: C   21 MET cc_start: 0.7780 (mmm) cc_final: 0.6905 (ttp)
REVERT: E   83 MET cc_start: 0.8753 (mtm) cc_final: 0.8242 (mtp)
REVERT: E   93 MET cc_start: 0.8768 (ttt) cc_final: 0.8223 (tpp)
REVERT: R  184 MET cc_start: 0.6991 (mmm) cc_final: 0.6622 (tpt)
REVERT: R  191 MET cc_start: 0.7411 (tpt) cc_final: 0.6830 (ttt)
REVERT: R  235 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8179 (mt)
REVERT: R  332 LEU cc_start: 0.8050 (mt) cc_final: 0.7801 (tp)
REVERT: R  345 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8124 (tp40)
  outliers start: 32
  outliers final: 20
  residues processed: 149
  average time/residue: 1.4633
  time to fit residues: 231.0215
Evaluate side-chains
  155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0170
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8420

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN
R 345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.170885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.135508 restraints weight = 9564.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.65
r_work: 0.3306 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9155  Z= 0.227
  Angle     :  0.502   6.927  12424  Z= 0.265
  Chirality :  0.042   0.143   1425
  Planarity :  0.004   0.049   1571
  Dihedral  :  4.685  59.172   1257
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 11.05 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.23 (0.25), residues: 1144
  helix:  2.41 (0.26), residues: 397
  sheet:  0.19 (0.30), residues: 279
  loop : -0.11 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.015   0.001   PHE A 196 
 TYR   0.011   0.001   TYR R 342 
 ARG   0.008   0.000   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8240 (mttt) cc_final: 0.7955 (mtmt)
REVERT: A   21 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7550 (mtm110)
REVERT: A   25 GLU cc_start: 0.7922 (tt0) cc_final: 0.7499 (tm-30)
REVERT: A  186 GLU cc_start: 0.7982 (tt0) cc_final: 0.7652 (mt-10)
REVERT: A  209 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7479 (pttp)
REVERT: A  276 GLU cc_start: 0.7198 (mp0) cc_final: 0.6917 (mp0)
REVERT: A  330 LYS cc_start: 0.7416 (mtmm) cc_final: 0.6066 (tttp)
REVERT: A  349 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7500 (ttmt)
REVERT: B   96 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7672 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8066 (mp0) cc_final: 0.7672 (tt0)
REVERT: B  137 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7438 (ttm-80)
REVERT: B  146 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8409 (mp)
REVERT: B  188 MET cc_start: 0.8691 (mmm) cc_final: 0.8344 (mmm)
REVERT: B  189 SER cc_start: 0.8170 (p) cc_final: 0.7765 (t)
REVERT: B  217 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.6958 (pp-130)
REVERT: B  219 ARG cc_start: 0.7342 (mmm160) cc_final: 0.6606 (mmt180)
REVERT: B  274 THR cc_start: 0.8794 (p) cc_final: 0.8559 (p)
REVERT: C   21 MET cc_start: 0.7821 (mmm) cc_final: 0.6913 (ttp)
REVERT: E   17 SER cc_start: 0.8341 (m) cc_final: 0.8118 (t)
REVERT: E   83 MET cc_start: 0.8796 (mtm) cc_final: 0.8217 (mtp)
REVERT: E   93 MET cc_start: 0.8855 (ttt) cc_final: 0.8324 (tpp)
REVERT: R  184 MET cc_start: 0.7040 (mmm) cc_final: 0.6688 (tpt)
REVERT: R  191 MET cc_start: 0.7454 (tpt) cc_final: 0.6893 (ttt)
REVERT: R  235 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8199 (mt)
REVERT: R  345 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8164 (tp40)
  outliers start: 27
  outliers final: 20
  residues processed: 148
  average time/residue: 1.5290
  time to fit residues: 239.8959
Evaluate side-chains
  154 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 2.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 38 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN
R 345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.171755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.136892 restraints weight = 9652.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.74
r_work: 0.3307 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9155  Z= 0.179
  Angle     :  0.482   7.294  12424  Z= 0.256
  Chirality :  0.041   0.143   1425
  Planarity :  0.004   0.049   1571
  Dihedral  :  4.612  57.268   1257
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.95 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.30 (0.25), residues: 1144
  helix:  2.50 (0.26), residues: 395
  sheet:  0.22 (0.30), residues: 284
  loop : -0.08 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.012   0.001   TYR R 342 
 ARG   0.009   0.000   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.078 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8224 (mttt) cc_final: 0.7946 (mtmt)
REVERT: A   21 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7550 (mtm110)
REVERT: A   25 GLU cc_start: 0.7955 (tt0) cc_final: 0.7578 (tt0)
REVERT: A  186 GLU cc_start: 0.7995 (tt0) cc_final: 0.7658 (mt-10)
REVERT: A  209 LYS cc_start: 0.7892 (pttp) cc_final: 0.7637 (pptt)
REVERT: A  276 GLU cc_start: 0.7218 (mp0) cc_final: 0.6981 (mp0)
REVERT: A  330 LYS cc_start: 0.7409 (mtmm) cc_final: 0.6058 (tttp)
REVERT: A  349 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7503 (ttmt)
REVERT: B   96 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7530 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8059 (mp0) cc_final: 0.7668 (tt0)
REVERT: B  137 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7481 (ttm-80)
REVERT: B  146 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8418 (mp)
REVERT: B  188 MET cc_start: 0.8680 (mmm) cc_final: 0.8339 (mmm)
REVERT: B  189 SER cc_start: 0.8140 (p) cc_final: 0.7734 (t)
REVERT: B  217 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.6964 (pp-130)
REVERT: B  219 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6586 (mmt180)
REVERT: B  274 THR cc_start: 0.8750 (p) cc_final: 0.8499 (p)
REVERT: C   21 MET cc_start: 0.7811 (mmm) cc_final: 0.6891 (ttp)
REVERT: E   17 SER cc_start: 0.8335 (m) cc_final: 0.8111 (t)
REVERT: E   83 MET cc_start: 0.8787 (mtm) cc_final: 0.8223 (mtp)
REVERT: E   93 MET cc_start: 0.8863 (ttt) cc_final: 0.8393 (tpp)
REVERT: E  179 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8033 (tt0)
REVERT: R  184 MET cc_start: 0.7017 (mmm) cc_final: 0.6656 (tpt)
REVERT: R  191 MET cc_start: 0.7455 (tpt) cc_final: 0.6878 (ttt)
REVERT: R  235 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8194 (mt)
REVERT: R  266 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7433 (mtt-85)
REVERT: R  345 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8114 (tp40)
  outliers start: 30
  outliers final: 19
  residues processed: 153
  average time/residue: 1.6214
  time to fit residues: 263.3886
Evaluate side-chains
  152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  179 GLN
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN
R 345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.171267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.135907 restraints weight = 9525.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.66
r_work: 0.3314 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9155  Z= 0.202
  Angle     :  0.503   8.901  12424  Z= 0.263
  Chirality :  0.042   0.154   1425
  Planarity :  0.004   0.048   1571
  Dihedral  :  4.645  56.619   1257
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.78 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.29 (0.25), residues: 1144
  helix:  2.48 (0.26), residues: 395
  sheet:  0.21 (0.30), residues: 290
  loop : -0.09 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.011   0.001   TYR R 342 
 ARG   0.009   0.000   ARG A 208 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8219 (mttt) cc_final: 0.7941 (mtmt)
REVERT: A   21 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7548 (mtm110)
REVERT: A   25 GLU cc_start: 0.7937 (tt0) cc_final: 0.7560 (tt0)
REVERT: A  186 GLU cc_start: 0.7972 (tt0) cc_final: 0.7649 (mt-10)
REVERT: A  209 LYS cc_start: 0.7886 (pttp) cc_final: 0.7615 (pptt)
REVERT: A  330 LYS cc_start: 0.7412 (mtmm) cc_final: 0.6050 (tttp)
REVERT: A  349 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7497 (ttmt)
REVERT: B   96 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7636 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8054 (mp0) cc_final: 0.7669 (tt0)
REVERT: B  146 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: B  188 MET cc_start: 0.8681 (mmm) cc_final: 0.8342 (mmm)
REVERT: B  189 SER cc_start: 0.8172 (p) cc_final: 0.7764 (t)
REVERT: B  217 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.6957 (pp-130)
REVERT: B  219 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6592 (mmt180)
REVERT: B  274 THR cc_start: 0.8794 (p) cc_final: 0.8557 (p)
REVERT: C   21 MET cc_start: 0.7847 (mmm) cc_final: 0.6922 (ttp)
REVERT: E   17 SER cc_start: 0.8342 (m) cc_final: 0.8123 (t)
REVERT: E   83 MET cc_start: 0.8793 (mtm) cc_final: 0.8234 (mtp)
REVERT: E   93 MET cc_start: 0.8854 (ttt) cc_final: 0.8385 (tpp)
REVERT: E  179 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8055 (tt0)
REVERT: R  184 MET cc_start: 0.7019 (mmm) cc_final: 0.6667 (tpt)
REVERT: R  191 MET cc_start: 0.7461 (tpt) cc_final: 0.6879 (ttt)
REVERT: R  235 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8197 (mt)
REVERT: R  266 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7437 (mtt-85)
REVERT: R  345 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8141 (tp40)
  outliers start: 26
  outliers final: 19
  residues processed: 148
  average time/residue: 1.4480
  time to fit residues: 227.1807
Evaluate side-chains
  150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  179 GLN
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  345 GLN
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 14 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0570
   chunk 97 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.171904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.136714 restraints weight = 9571.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.58
r_work: 0.3317 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9155  Z= 0.183
  Angle     :  0.500   7.612  12424  Z= 0.262
  Chirality :  0.042   0.155   1425
  Planarity :  0.004   0.048   1571
  Dihedral  :  4.603  55.027   1257
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.98 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.33 (0.25), residues: 1144
  helix:  2.51 (0.26), residues: 395
  sheet:  0.28 (0.30), residues: 287
  loop : -0.09 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.011   0.001   TYR R 341 
 ARG   0.009   0.000   ARG B 137 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8211 (mttt) cc_final: 0.7937 (mtmt)
REVERT: A   21 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7532 (mtm110)
REVERT: A   25 GLU cc_start: 0.7914 (tt0) cc_final: 0.7509 (tm-30)
REVERT: A  186 GLU cc_start: 0.7955 (tt0) cc_final: 0.7640 (mt-10)
REVERT: A  209 LYS cc_start: 0.7870 (pttp) cc_final: 0.7615 (pptt)
REVERT: A  276 GLU cc_start: 0.7213 (mp0) cc_final: 0.6990 (mp0)
REVERT: A  330 LYS cc_start: 0.7381 (mtmm) cc_final: 0.6056 (tttp)
REVERT: A  349 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7488 (ttmt)
REVERT: B   96 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7515 (mtt-85)
REVERT: B  130 GLU cc_start: 0.8037 (mp0) cc_final: 0.7667 (tt0)
REVERT: B  146 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8417 (mp)
REVERT: B  188 MET cc_start: 0.8670 (mmm) cc_final: 0.8334 (mmm)
REVERT: B  189 SER cc_start: 0.8130 (p) cc_final: 0.7715 (t)
REVERT: B  217 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.6946 (pp-130)
REVERT: B  219 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6619 (mmt180)
REVERT: B  274 THR cc_start: 0.8777 (p) cc_final: 0.8529 (p)
REVERT: C   21 MET cc_start: 0.7839 (mmm) cc_final: 0.6920 (ttp)
REVERT: E   17 SER cc_start: 0.8343 (m) cc_final: 0.8128 (t)
REVERT: E   83 MET cc_start: 0.8789 (mtm) cc_final: 0.8232 (mtp)
REVERT: E   93 MET cc_start: 0.8851 (ttt) cc_final: 0.8392 (tpp)
REVERT: E  179 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7852 (tt0)
REVERT: R  184 MET cc_start: 0.7005 (mmm) cc_final: 0.6652 (tpt)
REVERT: R  191 MET cc_start: 0.7439 (tpt) cc_final: 0.6868 (ttt)
REVERT: R  235 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8189 (mt)
REVERT: R  266 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7444 (mtt-85)
  outliers start: 23
  outliers final: 19
  residues processed: 142
  average time/residue: 1.5444
  time to fit residues: 232.3246
Evaluate side-chains
  148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  179 GLN
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  254 ILE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    0.0570
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 104 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 106 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN
B 293 ASN
R 345 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.172277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.136842 restraints weight = 9544.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 1.61
r_work: 0.3327 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9155  Z= 0.172
  Angle     :  0.487   7.675  12424  Z= 0.255
  Chirality :  0.041   0.147   1425
  Planarity :  0.004   0.048   1571
  Dihedral  :  4.526  52.313   1257
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.19 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  1.34 (0.25), residues: 1144
  helix:  2.53 (0.26), residues: 395
  sheet:  0.28 (0.30), residues: 287
  loop : -0.09 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.010   0.001   TYR R 342 
 ARG   0.009   0.000   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7748.61 seconds
wall clock time: 135 minutes 51.27 seconds (8151.27 seconds total)