Starting phenix.real_space_refine
on Wed Mar  4 03:50:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f0t_31404/03_2026/7f0t_31404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f0t_31404/03_2026/7f0t_31404.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f0t_31404/03_2026/7f0t_31404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f0t_31404/03_2026/7f0t_31404.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f0t_31404/03_2026/7f0t_31404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f0t_31404/03_2026/7f0t_31404.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.100
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3052 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5176      2.51       5
     N    1432      2.21       5
     O    1500      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8164
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 2242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2242
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 9, 'TRANS': 272}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1888
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2619
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
      Conformer: "B"
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          bond proxies already assigned to first conformer: 2640
    Chain: "D"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "E"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ACYS B 233 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS B 233 " occ=0.50
    residue:
      pdb=" N  ACYS B 271 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS B 271 " occ=0.50
  Time building chain proxies: 2.31, per 1000 atoms: 0.28
  Number of scatterers: 8164
  At special positions: 0
  Unit cell: (78.264, 97.83, 127.179, 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      56     16.00
     O    1500      8.00
     N    1432      7.00
     C    5176      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " 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: 0.67
  Conformation dependent library (CDL) restraints added in 411.1 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      44.4% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'F' and resid 21 through 51
      removed outlier: 3.608A  pdb=" N   PHE F  51 " --> pdb=" O   ALA F  47 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  79  - end of helix
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.773A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR F 108 " --> pdb=" O   ILE F 104 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN F 113 " --> pdb=" O   ALA F 109 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
    Processing helix  chain 'F' and resid 136 through 161
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
    Processing helix  chain 'F' and resid 203 through 241
    Processing helix  chain 'F' and resid 265 through 299
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.878A  pdb=" N   GLY F 320 " --> pdb=" O   PHE F 316 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   TRP F 321 " --> pdb=" O   VAL F 317 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'A' and resid 13 through 40
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.808A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.949A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.803A  pdb=" N   PHE A 312 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.301A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.967A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.890A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.682A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.583A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.511A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS A 220 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.781A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.645A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.905A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.918A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.752A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.135A  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: 6.809A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.322A  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 232
      removed outlier: 6.846A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.024A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.474A  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 58 through 60
      removed outlier: 6.527A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ASP E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   MET E  34 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)

    433 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1361
        1.32 -     1.45: 2350
        1.45 -     1.57: 4547
        1.57 -     1.70: 0
        1.70 -     1.83: 75
  Bond restraints: 8333
  Sorted by residual:
  bond pdb=" CA  PHE F 288 "
       pdb=" C   PHE F 288 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.080 1.27e-02 6.20e+03 4.01e+01
  bond pdb=" CA  ASN F 292 "
       pdb=" C   ASN F 292 "
    ideal  model  delta    sigma   weight residual
    1.522  1.466  0.056 1.39e-02 5.18e+03 1.61e+01
  bond pdb=" C   ASN F 292 "
       pdb=" O   ASN F 292 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.047 1.24e-02 6.50e+03 1.44e+01
  bond pdb=" C   LEU F 291 "
       pdb=" O   LEU F 291 "
    ideal  model  delta    sigma   weight residual
    1.237  1.192  0.044 1.19e-02 7.06e+03 1.38e+01
  bond pdb=" C   PHE F 288 "
       pdb=" N   PHE F 289 "
    ideal  model  delta    sigma   weight residual
    1.335  1.293  0.042 1.38e-02 5.25e+03 9.40e+00
  ... (remaining 8328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 11047
        2.87 -     5.75: 211
        5.75 -     8.62: 22
        8.62 -    11.50: 4
       11.50 -    14.37: 1
  Bond angle restraints: 11285
  Sorted by residual:
  angle pdb=" N   ASN F 292 "
        pdb=" CA  ASN F 292 "
        pdb=" C   ASN F 292 "
      ideal   model   delta    sigma   weight residual
     111.75  103.61    8.14 1.28e+00 6.10e-01 4.05e+01
  angle pdb=" N   PHE F 288 "
        pdb=" CA  PHE F 288 "
        pdb=" C   PHE F 288 "
      ideal   model   delta    sigma   weight residual
     111.07  104.91    6.16 1.07e+00 8.73e-01 3.31e+01
  angle pdb=" C   LYS A 233 "
        pdb=" N   TRP A 234 "
        pdb=" CA  TRP A 234 "
      ideal   model   delta    sigma   weight residual
     121.94  110.63   11.31 2.00e+00 2.50e-01 3.20e+01
  angle pdb=" C   PHE A 222 "
        pdb=" CA  PHE A 222 "
        pdb=" CB  PHE A 222 "
      ideal   model   delta    sigma   weight residual
     109.35   98.97   10.38 1.98e+00 2.55e-01 2.75e+01
  angle pdb=" C   ARG A 232 "
        pdb=" N   LYS A 233 "
        pdb=" CA  LYS A 233 "
      ideal   model   delta    sigma   weight residual
     122.42  114.43    7.99 1.77e+00 3.19e-01 2.04e+01
  ... (remaining 11280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 4439
       17.24 -    34.48: 420
       34.48 -    51.72: 91
       51.72 -    68.95: 11
       68.95 -    86.19: 10
  Dihedral angle restraints: 4971
    sinusoidal: 1952
      harmonic: 3019
  Sorted by residual:
  dihedral pdb=" CB  CYS E  99 "
           pdb=" SG  CYS E  99 "
           pdb=" SG  CYS E 107 "
           pdb=" CB  CYS E 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    9.83   83.17     1      1.00e+01 1.00e-02 8.46e+01
  dihedral pdb=" C   PHE F 289 "
           pdb=" N   PHE F 289 "
           pdb=" CA  PHE F 289 "
           pdb=" CB  PHE F 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.04   14.44     0      2.50e+00 1.60e-01 3.34e+01
  dihedral pdb=" CA  PHE F  95 "
           pdb=" C   PHE F  95 "
           pdb=" N   CYS F  96 "
           pdb=" CA  CYS F  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.30  -27.70     0      5.00e+00 4.00e-02 3.07e+01
  ... (remaining 4968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.133: 1225
       0.133 -    0.266: 43
       0.266 -    0.399: 0
       0.399 -    0.532: 0
       0.532 -    0.665: 1
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CA  PHE F 289 "
            pdb=" N   PHE F 289 "
            pdb=" C   PHE F 289 "
            pdb=" CB  PHE F 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.85    0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" CA  ILE F 290 "
            pdb=" N   ILE F 290 "
            pdb=" C   ILE F 290 "
            pdb=" CB  ILE F 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.18    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  ASP B 290 "
            pdb=" N   ASP B 290 "
            pdb=" C   ASP B 290 "
            pdb=" CB  ASP B 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1266 not shown)

  Planarity restraints: 1437
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  28 "    0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   LYS A  28 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   LYS A  28 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLN A  29 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 201 "    0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   ILE F 201 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ILE F 201 "    0.022 2.00e-02 2.50e+03
        pdb=" N   SER F 202 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  25 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.02e+00
        pdb=" C   LYS A  25 "    0.049 2.00e-02 2.50e+03
        pdb=" O   LYS A  25 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE A  26 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1434 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 140
        2.63 -     3.20: 7853
        3.20 -     3.77: 12590
        3.77 -     4.33: 17453
        4.33 -     4.90: 29162
  Nonbonded interactions: 67198
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.065 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" O   PRO E 100 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" OE2 GLU A  27 "
            pdb=" NZ  LYS B  89 "
     model   vdw
     2.126 3.120
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.143 3.040
  ... (remaining 67193 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.080   8336  Z= 0.464
  Angle     :  1.018  14.375  11291  Z= 0.591
  Chirality :  0.062   0.665   1269
  Planarity :  0.006   0.057   1437
  Dihedral  : 14.291  86.194   3002
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 14.04 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.22), residues: 1021
  helix: -1.79 (0.20), residues: 416
  sheet: -1.31 (0.31), residues: 228
  loop : -1.44 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  42 
 TYR   0.020   0.003   TYR A 311 
 PHE   0.031   0.003   PHE B 199 
 TRP   0.034   0.003   TRP B 169 
 HIS   0.022   0.003   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.01014 ( 8333)
  covalent geometry    : angle       1.01535 (11285)
  SS BOND              : bond        0.00525 (    3)
  SS BOND              : angle       3.19582 (    6)
  hydrogen bonds       : bond        0.14295 (  433)
  hydrogen bonds       : angle       7.16960 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 187
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7853 (mmt90) cc_final: 0.6895 (tpm170)
REVERT: F   57 LYS cc_start: 0.8526 (mppt) cc_final: 0.8263 (mtpt)
REVERT: F   90 TRP cc_start: 0.8475 (t-100) cc_final: 0.8260 (t-100)
REVERT: F  225 ILE cc_start: 0.8918 (mm) cc_final: 0.8612 (mt)
REVERT: A   13 ARG cc_start: 0.8037 (pmt170) cc_final: 0.7799 (ptt-90)
REVERT: A  211 LYS cc_start: 0.8732 (mttm) cc_final: 0.8481 (mttp)
REVERT: A  221 MET cc_start: 0.8366 (ttp) cc_final: 0.8062 (ttp)
REVERT: A  229 ASP cc_start: 0.7786 (m-30) cc_final: 0.6766 (t70)
REVERT: A  317 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7252 (mtm110)
REVERT: A  318 TYR cc_start: 0.7433 (t80) cc_final: 0.7206 (t80)
REVERT: B   68 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7433 (ttt-90)
REVERT: B  325 MET cc_start: 0.7570 (tpp) cc_final: 0.7277 (tpp)
REVERT: D   59 ASN cc_start: 0.8676 (t0) cc_final: 0.8219 (t0)
REVERT: E   82 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7257 (tm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 192
  average time/residue: 0.1103
  time to fit residues: 27.0051
Evaluate side-chains
  152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  290 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain D residue    9 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
F 113 ASN
F 164 HIS
F 237 HIS
F 240 ASN
F 323 ASN
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 HIS
A 371 ASN
B  88 ASN
B 155 ASN
B 175 GLN
B 340 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115942 restraints weight = 22435.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 4.43
r_work: 0.3274 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8336  Z= 0.145
  Angle     :  0.599  11.473  11291  Z= 0.322
  Chirality :  0.044   0.150   1269
  Planarity :  0.004   0.039   1437
  Dihedral  :  5.450  48.606   1139
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.29 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.25), residues: 1021
  helix:  0.48 (0.24), residues: 411
  sheet: -0.76 (0.33), residues: 231
  loop : -0.86 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.014   0.002   TYR A  37 
 PHE   0.015   0.001   PHE F 289 
 TRP   0.028   0.002   TRP B 169 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8333)
  covalent geometry    : angle       0.59811 (11285)
  SS BOND              : bond        0.00448 (    3)
  SS BOND              : angle       1.41903 (    6)
  hydrogen bonds       : bond        0.05090 (  433)
  hydrogen bonds       : angle       5.24932 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7729 (mmt90) cc_final: 0.6644 (tpm170)
REVERT: F   90 TRP cc_start: 0.8450 (t-100) cc_final: 0.8053 (t-100)
REVERT: F  190 LEU cc_start: 0.8698 (mt) cc_final: 0.8380 (mp)
REVERT: F  309 ASP cc_start: 0.7557 (t70) cc_final: 0.7271 (t70)
REVERT: F  319 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7306 (m-10)
REVERT: A   13 ARG cc_start: 0.8460 (pmt170) cc_final: 0.8247 (ptt-90)
REVERT: A   17 LYS cc_start: 0.8938 (tptt) cc_final: 0.8696 (tppt)
REVERT: A  211 LYS cc_start: 0.8823 (mttm) cc_final: 0.8537 (mttp)
REVERT: A  229 ASP cc_start: 0.8095 (m-30) cc_final: 0.7820 (m-30)
REVERT: A  252 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6343 (t70)
REVERT: A  318 TYR cc_start: 0.7061 (t80) cc_final: 0.6849 (t80)
REVERT: A  327 GLU cc_start: 0.7770 (mp0) cc_final: 0.7515 (mp0)
REVERT: A  370 GLU cc_start: 0.8330 (pm20) cc_final: 0.8001 (pm20)
REVERT: B   61 MET cc_start: 0.8905 (ppp) cc_final: 0.8664 (ppp)
REVERT: B   68 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7097 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8880 (t80) cc_final: 0.8669 (t80)
REVERT: B  132 ASN cc_start: 0.7794 (m-40) cc_final: 0.6977 (p0)
REVERT: B  205 ASP cc_start: 0.8352 (p0) cc_final: 0.8101 (p0)
REVERT: B  292 PHE cc_start: 0.8604 (m-80) cc_final: 0.8340 (m-80)
REVERT: B  325 MET cc_start: 0.7648 (tpp) cc_final: 0.7362 (tpp)
REVERT: E   80 TYR cc_start: 0.7944 (m-80) cc_final: 0.7439 (m-80)
REVERT: E   82 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6738 (tm-30)
REVERT: E  120 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7767 (mt0)
  outliers start: 22
  outliers final: 16
  residues processed: 184
  average time/residue: 0.0943
  time to fit residues: 22.9241
Evaluate side-chains
  163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  161 LEU
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  290 ILE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  107 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.149163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.111640 restraints weight = 25057.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 4.68
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8336  Z= 0.173
  Angle     :  0.578  11.343  11291  Z= 0.307
  Chirality :  0.044   0.199   1269
  Planarity :  0.004   0.043   1437
  Dihedral  :  4.961  47.455   1134
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.55 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.26), residues: 1021
  helix:  1.31 (0.25), residues: 410
  sheet: -0.52 (0.33), residues: 227
  loop : -0.68 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.016   0.001   TYR A 253 
 PHE   0.015   0.001   PHE F 289 
 TRP   0.025   0.002   TRP B 169 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8333)
  covalent geometry    : angle       0.57681 (11285)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       1.47203 (    6)
  hydrogen bonds       : bond        0.04773 (  433)
  hydrogen bonds       : angle       4.97457 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7480 (mmt90) cc_final: 0.6529 (tpm170)
REVERT: F   85 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8140 (mm-30)
REVERT: F   90 TRP cc_start: 0.8332 (t-100) cc_final: 0.7998 (t-100)
REVERT: F  225 ILE cc_start: 0.8685 (mt) cc_final: 0.8456 (mt)
REVERT: F  309 ASP cc_start: 0.7601 (t70) cc_final: 0.7294 (t70)
REVERT: A   17 LYS cc_start: 0.8978 (tptt) cc_final: 0.8688 (tppt)
REVERT: A   38 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7862 (ttp-110)
REVERT: A  211 LYS cc_start: 0.8726 (mttm) cc_final: 0.8514 (mttp)
REVERT: A  229 ASP cc_start: 0.7968 (m-30) cc_final: 0.7657 (m-30)
REVERT: A  318 TYR cc_start: 0.7134 (t80) cc_final: 0.6501 (t80)
REVERT: A  327 GLU cc_start: 0.7903 (mp0) cc_final: 0.7600 (mp0)
REVERT: B   68 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7033 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8888 (t80) cc_final: 0.8529 (t80)
REVERT: B  132 ASN cc_start: 0.7766 (m-40) cc_final: 0.6938 (p0)
REVERT: B  292 PHE cc_start: 0.8627 (m-80) cc_final: 0.8321 (m-80)
REVERT: B  297 TRP cc_start: 0.8494 (m100) cc_final: 0.8136 (m100)
REVERT: B  325 MET cc_start: 0.7849 (tpp) cc_final: 0.7446 (tpp)
REVERT: E   80 TYR cc_start: 0.7844 (m-80) cc_final: 0.7131 (m-80)
REVERT: E   82 GLN cc_start: 0.7036 (tm-30) cc_final: 0.6686 (tm-30)
  outliers start: 29
  outliers final: 25
  residues processed: 163
  average time/residue: 0.0924
  time to fit residues: 19.7780
Evaluate side-chains
  164 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  107 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0670
   chunk 17 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
F 323 ASN
F 327 ASN
A  23 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.153283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.115231 restraints weight = 31118.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 5.20
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8336  Z= 0.119
  Angle     :  0.529  12.127  11291  Z= 0.278
  Chirality :  0.042   0.144   1269
  Planarity :  0.003   0.044   1437
  Dihedral  :  4.582  42.458   1132
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.78 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.26), residues: 1021
  helix:  1.80 (0.25), residues: 406
  sheet: -0.37 (0.33), residues: 219
  loop : -0.68 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  42 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.011   0.001   PHE F 289 
 TRP   0.023   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8333)
  covalent geometry    : angle       0.52908 (11285)
  SS BOND              : bond        0.00248 (    3)
  SS BOND              : angle       1.05878 (    6)
  hydrogen bonds       : bond        0.04221 (  433)
  hydrogen bonds       : angle       4.67691 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7394 (mmt90) cc_final: 0.6401 (tpm170)
REVERT: F  225 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8466 (mt)
REVERT: F  319 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7146 (m-10)
REVERT: A   17 LYS cc_start: 0.8965 (tptt) cc_final: 0.8715 (tppt)
REVERT: A  229 ASP cc_start: 0.8053 (m-30) cc_final: 0.7762 (m-30)
REVERT: A  239 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8635 (p0)
REVERT: A  252 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6170 (t70)
REVERT: A  317 ARG cc_start: 0.7513 (mtp-110) cc_final: 0.7180 (ttp80)
REVERT: A  318 TYR cc_start: 0.7012 (t80) cc_final: 0.6443 (t80)
REVERT: A  327 GLU cc_start: 0.7872 (mp0) cc_final: 0.7530 (mp0)
REVERT: A  370 GLU cc_start: 0.8191 (pm20) cc_final: 0.7731 (pm20)
REVERT: A  390 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8301 (tp-100)
REVERT: B   68 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7187 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8805 (t80) cc_final: 0.8397 (t80)
REVERT: B  132 ASN cc_start: 0.7600 (m-40) cc_final: 0.6793 (p0)
REVERT: B  292 PHE cc_start: 0.8430 (m-80) cc_final: 0.8148 (m-80)
REVERT: B  297 TRP cc_start: 0.8437 (m100) cc_final: 0.7569 (m100)
REVERT: B  325 MET cc_start: 0.7823 (tpp) cc_final: 0.7399 (tpp)
REVERT: E   19 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7893 (mmm-85)
REVERT: E   82 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6804 (tm-30)
REVERT: E  120 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7690 (mm-40)
  outliers start: 35
  outliers final: 27
  residues processed: 185
  average time/residue: 0.0916
  time to fit residues: 22.3892
Evaluate side-chains
  175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  225 ILE
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.152301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.115248 restraints weight = 23320.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 4.55
r_work: 0.3274 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8336  Z= 0.128
  Angle     :  0.526  11.482  11291  Z= 0.278
  Chirality :  0.042   0.143   1269
  Planarity :  0.004   0.058   1437
  Dihedral  :  4.471  38.321   1132
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 17.67 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.26), residues: 1021
  helix:  2.05 (0.25), residues: 409
  sheet: -0.38 (0.33), residues: 218
  loop : -0.64 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 219 
 TYR   0.020   0.001   TYR A  37 
 PHE   0.012   0.001   PHE F 289 
 TRP   0.021   0.001   TRP B 169 
 HIS   0.005   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8333)
  covalent geometry    : angle       0.52525 (11285)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.97107 (    6)
  hydrogen bonds       : bond        0.04185 (  433)
  hydrogen bonds       : angle       4.61301 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7493 (mmt90) cc_final: 0.6509 (tpm170)
REVERT: F  225 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8487 (mt)
REVERT: F  319 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7144 (m-10)
REVERT: A   17 LYS cc_start: 0.8938 (tptt) cc_final: 0.8666 (tppt)
REVERT: A  229 ASP cc_start: 0.8234 (m-30) cc_final: 0.7917 (m-30)
REVERT: A  239 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8788 (p0)
REVERT: A  252 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6224 (t70)
REVERT: A  317 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7507 (ttp80)
REVERT: A  318 TYR cc_start: 0.7057 (t80) cc_final: 0.6474 (t80)
REVERT: A  327 GLU cc_start: 0.7910 (mp0) cc_final: 0.7554 (mp0)
REVERT: A  370 GLU cc_start: 0.8292 (pm20) cc_final: 0.7865 (pm20)
REVERT: A  390 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8450 (tp-100)
REVERT: B   61 MET cc_start: 0.8828 (ppp) cc_final: 0.8561 (ppp)
REVERT: B  105 TYR cc_start: 0.8778 (t80) cc_final: 0.8358 (t80)
REVERT: B  292 PHE cc_start: 0.8491 (m-80) cc_final: 0.8257 (m-80)
REVERT: B  297 TRP cc_start: 0.8552 (m100) cc_final: 0.7732 (m100)
REVERT: B  325 MET cc_start: 0.7781 (tpp) cc_final: 0.7405 (tpp)
REVERT: E   19 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7901 (mmm-85)
REVERT: E   82 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6904 (tm-30)
REVERT: E  120 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8044 (mm-40)
  outliers start: 39
  outliers final: 31
  residues processed: 177
  average time/residue: 0.0895
  time to fit residues: 21.4462
Evaluate side-chains
  176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  225 ILE
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.3980
   chunk 39 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0010
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.154623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116929 restraints weight = 26819.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 4.89
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3474
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3474
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8336  Z= 0.109
  Angle     :  0.516  11.945  11291  Z= 0.268
  Chirality :  0.041   0.145   1269
  Planarity :  0.004   0.045   1437
  Dihedral  :  4.298  33.007   1132
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 18.46 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.26), residues: 1021
  helix:  2.22 (0.25), residues: 408
  sheet: -0.30 (0.33), residues: 223
  loop : -0.57 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 219 
 TYR   0.022   0.001   TYR A  37 
 PHE   0.013   0.001   PHE E  29 
 TRP   0.020   0.001   TRP B 169 
 HIS   0.010   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 8333)
  covalent geometry    : angle       0.51538 (11285)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       0.78113 (    6)
  hydrogen bonds       : bond        0.03939 (  433)
  hydrogen bonds       : angle       4.47943 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 158
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7427 (mmt90) cc_final: 0.6414 (tpm170)
REVERT: F  225 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: F  319 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7115 (m-10)
REVERT: A  229 ASP cc_start: 0.8034 (m-30) cc_final: 0.7699 (m-30)
REVERT: A  239 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8676 (p0)
REVERT: A  252 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6065 (t70)
REVERT: A  318 TYR cc_start: 0.6965 (t80) cc_final: 0.6359 (t80)
REVERT: A  327 GLU cc_start: 0.7938 (mp0) cc_final: 0.7600 (mp0)
REVERT: A  370 GLU cc_start: 0.8162 (pm20) cc_final: 0.7707 (pm20)
REVERT: A  390 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8197 (tp-100)
REVERT: B   61 MET cc_start: 0.8329 (ppp) cc_final: 0.8089 (ppp)
REVERT: B  105 TYR cc_start: 0.8655 (t80) cc_final: 0.8225 (t80)
REVERT: B  120 ILE cc_start: 0.8428 (mt) cc_final: 0.7963 (mm)
REVERT: B  292 PHE cc_start: 0.8348 (m-80) cc_final: 0.8049 (m-80)
REVERT: B  297 TRP cc_start: 0.8403 (m100) cc_final: 0.7727 (m100)
REVERT: B  325 MET cc_start: 0.7786 (tpp) cc_final: 0.7380 (tpp)
REVERT: E   19 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7802 (mmm-85)
REVERT: E   52 SER cc_start: 0.7977 (t) cc_final: 0.6913 (m)
REVERT: E  120 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7585 (mt0)
  outliers start: 41
  outliers final: 33
  residues processed: 185
  average time/residue: 0.0879
  time to fit residues: 21.9482
Evaluate side-chains
  186 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain F residue   85 GLU
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  225 ILE
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  330 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 86 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
F  53 HIS
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.149645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112160 restraints weight = 25832.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 4.73
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3408
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3408 r_free = 0.3408    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3408
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8336  Z= 0.172
  Angle     :  0.558  11.539  11291  Z= 0.293
  Chirality :  0.043   0.142   1269
  Planarity :  0.004   0.046   1437
  Dihedral  :  4.460  34.159   1132
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.14 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.26), residues: 1021
  helix:  2.09 (0.25), residues: 406
  sheet: -0.43 (0.33), residues: 224
  loop : -0.55 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.022   0.002   TYR A  37 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.012   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8333)
  covalent geometry    : angle       0.55738 (11285)
  SS BOND              : bond        0.00294 (    3)
  SS BOND              : angle       1.14901 (    6)
  hydrogen bonds       : bond        0.04323 (  433)
  hydrogen bonds       : angle       4.65997 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7334 (mmt90) cc_final: 0.6365 (tpm170)
REVERT: F  225 ILE cc_start: 0.8745 (mt) cc_final: 0.8517 (mt)
REVERT: F  319 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7254 (m-10)
REVERT: A  229 ASP cc_start: 0.7962 (m-30) cc_final: 0.7593 (m-30)
REVERT: A  252 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6262 (t70)
REVERT: A  318 TYR cc_start: 0.7227 (t80) cc_final: 0.6626 (t80)
REVERT: A  327 GLU cc_start: 0.8089 (mp0) cc_final: 0.7740 (mp0)
REVERT: A  370 GLU cc_start: 0.8209 (pm20) cc_final: 0.7789 (pm20)
REVERT: A  390 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8233 (tp-100)
REVERT: B   61 MET cc_start: 0.8434 (ppp) cc_final: 0.8231 (ppp)
REVERT: B  105 TYR cc_start: 0.8836 (t80) cc_final: 0.8334 (t80)
REVERT: B  254 ASP cc_start: 0.7766 (t70) cc_final: 0.7267 (t0)
REVERT: B  292 PHE cc_start: 0.8506 (m-80) cc_final: 0.8214 (m-80)
REVERT: B  325 MET cc_start: 0.7977 (tpp) cc_final: 0.7534 (tpp)
REVERT: E   52 SER cc_start: 0.8276 (t) cc_final: 0.7177 (m)
REVERT: E  120 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7617 (mt0)
  outliers start: 44
  outliers final: 39
  residues processed: 178
  average time/residue: 0.0855
  time to fit residues: 20.9053
Evaluate side-chains
  189 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   53 HIS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  283 CYS
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  330 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 77 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   chunk 52 optimal weight:   20.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.152067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.113333 restraints weight = 37907.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 5.60
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8336  Z= 0.117
  Angle     :  0.528  11.695  11291  Z= 0.275
  Chirality :  0.042   0.145   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.363  31.821   1132
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 20.50 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.26), residues: 1021
  helix:  2.24 (0.25), residues: 410
  sheet: -0.40 (0.33), residues: 224
  loop : -0.49 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.021   0.001   TYR A  37 
 PHE   0.012   0.001   PHE E  29 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.013   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8333)
  covalent geometry    : angle       0.52763 (11285)
  SS BOND              : bond        0.00342 (    3)
  SS BOND              : angle       1.11130 (    6)
  hydrogen bonds       : bond        0.04030 (  433)
  hydrogen bonds       : angle       4.51414 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 155
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7520 (mmt90) cc_final: 0.6374 (tpm170)
REVERT: F  225 ILE cc_start: 0.8776 (mt) cc_final: 0.8424 (mt)
REVERT: F  319 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7146 (m-10)
REVERT: A  229 ASP cc_start: 0.8001 (m-30) cc_final: 0.7647 (m-30)
REVERT: A  252 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6291 (t70)
REVERT: A  318 TYR cc_start: 0.7112 (t80) cc_final: 0.6549 (t80)
REVERT: A  327 GLU cc_start: 0.8096 (mp0) cc_final: 0.7744 (mp0)
REVERT: A  370 GLU cc_start: 0.8246 (pm20) cc_final: 0.7814 (pm20)
REVERT: A  390 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8214 (tp-100)
REVERT: B  105 TYR cc_start: 0.8785 (t80) cc_final: 0.8360 (t80)
REVERT: B  212 ASP cc_start: 0.7710 (t0) cc_final: 0.7040 (t0)
REVERT: B  254 ASP cc_start: 0.7710 (t70) cc_final: 0.7171 (t0)
REVERT: B  292 PHE cc_start: 0.8466 (m-80) cc_final: 0.8201 (m-80)
REVERT: B  297 TRP cc_start: 0.8456 (m100) cc_final: 0.7805 (m100)
REVERT: B  325 MET cc_start: 0.8006 (tpp) cc_final: 0.7605 (tpp)
REVERT: E   52 SER cc_start: 0.8191 (t) cc_final: 0.7091 (m)
REVERT: E   73 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7284 (t70)
REVERT: E  120 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7617 (mt0)
  outliers start: 40
  outliers final: 36
  residues processed: 184
  average time/residue: 0.0821
  time to fit residues: 20.6074
Evaluate side-chains
  185 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 146
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  283 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  107 CYS
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 84 optimal weight:   20.0000
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.151424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.113402 restraints weight = 32262.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 5.21
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8336  Z= 0.136
  Angle     :  0.537  11.549  11291  Z= 0.280
  Chirality :  0.042   0.141   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.362  31.528   1132
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.27 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.26), residues: 1021
  helix:  2.26 (0.25), residues: 409
  sheet: -0.37 (0.33), residues: 223
  loop : -0.48 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.020   0.001   TYR A  37 
 PHE   0.012   0.001   PHE F 289 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8333)
  covalent geometry    : angle       0.53675 (11285)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       1.03580 (    6)
  hydrogen bonds       : bond        0.04047 (  433)
  hydrogen bonds       : angle       4.51285 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 146
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7327 (mmt90) cc_final: 0.6204 (tpm170)
REVERT: F  225 ILE cc_start: 0.8748 (mt) cc_final: 0.8509 (mt)
REVERT: F  319 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7147 (m-10)
REVERT: A  229 ASP cc_start: 0.8017 (m-30) cc_final: 0.7659 (m-30)
REVERT: A  239 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8805 (p0)
REVERT: A  252 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6250 (t70)
REVERT: A  318 TYR cc_start: 0.7219 (t80) cc_final: 0.6630 (t80)
REVERT: A  327 GLU cc_start: 0.8100 (mp0) cc_final: 0.7758 (mp0)
REVERT: A  370 GLU cc_start: 0.8296 (pm20) cc_final: 0.7902 (pm20)
REVERT: A  390 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8218 (tp-100)
REVERT: B  105 TYR cc_start: 0.8793 (t80) cc_final: 0.8370 (t80)
REVERT: B  254 ASP cc_start: 0.7746 (t70) cc_final: 0.7215 (t0)
REVERT: B  292 PHE cc_start: 0.8549 (m-80) cc_final: 0.8245 (m-80)
REVERT: B  297 TRP cc_start: 0.8460 (m100) cc_final: 0.7812 (m100)
REVERT: B  325 MET cc_start: 0.8034 (tpp) cc_final: 0.7554 (tpp)
REVERT: E   52 SER cc_start: 0.8184 (t) cc_final: 0.7160 (m)
REVERT: E   73 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7218 (t70)
REVERT: E  120 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7630 (mt0)
  outliers start: 43
  outliers final: 36
  residues processed: 178
  average time/residue: 0.0806
  time to fit residues: 19.8386
Evaluate side-chains
  184 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  283 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 67 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.153113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.114760 restraints weight = 34409.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 5.37
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8336  Z= 0.118
  Angle     :  0.529  11.588  11291  Z= 0.275
  Chirality :  0.042   0.144   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.326  30.226   1132
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.27 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.26), residues: 1021
  helix:  2.33 (0.25), residues: 409
  sheet: -0.29 (0.33), residues: 223
  loop : -0.48 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.020   0.001   TYR A  37 
 PHE   0.011   0.001   PHE F 289 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8333)
  covalent geometry    : angle       0.52912 (11285)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       0.93903 (    6)
  hydrogen bonds       : bond        0.03925 (  433)
  hydrogen bonds       : angle       4.45113 ( 1245)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 147
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7320 (mmt90) cc_final: 0.6120 (tpm170)
REVERT: F  225 ILE cc_start: 0.8734 (mt) cc_final: 0.8490 (mt)
REVERT: F  319 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7149 (m-10)
REVERT: A  229 ASP cc_start: 0.7956 (m-30) cc_final: 0.7585 (m-30)
REVERT: A  239 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8766 (p0)
REVERT: A  252 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6240 (t70)
REVERT: A  318 TYR cc_start: 0.7145 (t80) cc_final: 0.6662 (t80)
REVERT: A  327 GLU cc_start: 0.8106 (mp0) cc_final: 0.7768 (mp0)
REVERT: A  370 GLU cc_start: 0.8261 (pm20) cc_final: 0.7852 (pm20)
REVERT: A  390 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8227 (tp-100)
REVERT: B  105 TYR cc_start: 0.8763 (t80) cc_final: 0.8536 (t80)
REVERT: B  254 ASP cc_start: 0.7718 (t70) cc_final: 0.7186 (t0)
REVERT: B  292 PHE cc_start: 0.8492 (m-80) cc_final: 0.8177 (m-80)
REVERT: B  297 TRP cc_start: 0.8461 (m100) cc_final: 0.7868 (m100)
REVERT: B  325 MET cc_start: 0.8032 (tpp) cc_final: 0.7581 (tpp)
REVERT: E   52 SER cc_start: 0.8094 (t) cc_final: 0.7075 (m)
REVERT: E   73 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7244 (t0)
REVERT: E  120 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7525 (mt0)
  outliers start: 43
  outliers final: 36
  residues processed: 179
  average time/residue: 0.0856
  time to fit residues: 21.3071
Evaluate side-chains
  183 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 143
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  283 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0060
   chunk 41 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 79 optimal weight:    0.2980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
F 327 ASN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.154322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.117269 restraints weight = 23596.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 4.60
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3476
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3476
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8336  Z= 0.111
  Angle     :  0.521  11.440  11291  Z= 0.271
  Chirality :  0.042   0.140   1269
  Planarity :  0.003   0.042   1437
  Dihedral  :  4.237  29.111   1132
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 20.95 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.26), residues: 1021
  helix:  2.36 (0.25), residues: 409
  sheet: -0.13 (0.33), residues: 221
  loop : -0.45 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.020   0.001   TYR A  37 
 PHE   0.011   0.001   PHE F 289 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8333)
  covalent geometry    : angle       0.52086 (11285)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.84581 (    6)
  hydrogen bonds       : bond        0.03849 (  433)
  hydrogen bonds       : angle       4.41654 ( 1245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1899.14 seconds
wall clock time: 33 minutes 18.98 seconds (1998.98 seconds total)