Starting phenix.real_space_refine
on Mon Jul 28 19:33:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f0t_31404/07_2025/7f0t_31404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f0t_31404/07_2025/7f0t_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f0t_31404/07_2025/7f0t_31404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f0t_31404/07_2025/7f0t_31404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f0t_31404/07_2025/7f0t_31404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f0t_31404/07_2025/7f0t_31404.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 1, 'ASP:plan': 2}
          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: 5.61, per 1000 atoms: 0.69
  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: 2.07
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.82
  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: 2.15

  Time building geometry restraints manager: 2.36 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:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.110
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.660
-------------------------------------------------------------------------------
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 : 13.17
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (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
 TRP   0.034   0.003   TRP B 169 
 HIS   0.022   0.003   HIS A 357 
 PHE   0.031   0.003   PHE B 199 
 TYR   0.020   0.003   TYR A 311 
 ARG   0.006   0.001   ARG A  42 

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

*********************** 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  : 0.901 
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: 0.2653
  time to fit residues: 64.7901
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  : 1.005 
-------------------------------------------------------------------------------
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 84 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.115300 restraints weight = 24408.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 4.62
r_work: 0.3265 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.1796

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= 0.146
  Angle     :  0.598  11.474  11291  Z= 0.321
  Chirality :  0.044   0.147   1269
  Planarity :  0.004   0.039   1437
  Dihedral  :  5.464  48.804   1139
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.72 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.25), residues: 1021
  helix:  0.49 (0.24), residues: 411
  sheet: -0.76 (0.33), residues: 231
  loop : -0.85 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 169 
 HIS   0.009   0.002   HIS A 357 
 PHE   0.015   0.001   PHE F 289 
 TYR   0.014   0.002   TYR A  37 
 ARG   0.005   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05090 (  433)
  hydrogen bonds       : angle       5.24207 ( 1245)
  SS BOND              : bond        0.00368 (    3)
  SS BOND              : angle       1.43509 (    6)
  covalent geometry    : bond        0.00311 ( 8333)
  covalent geometry    : angle       0.59709 (11285)

*********************** 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
  192 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7736 (mmt90) cc_final: 0.6651 (tpm170)
REVERT: F   90 TRP cc_start: 0.8434 (t-100) cc_final: 0.8031 (t-100)
REVERT: F  190 LEU cc_start: 0.8694 (mt) cc_final: 0.8378 (mp)
REVERT: F  309 ASP cc_start: 0.7594 (t70) cc_final: 0.7311 (t70)
REVERT: F  319 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7303 (m-10)
REVERT: A   13 ARG cc_start: 0.8459 (pmt170) cc_final: 0.8240 (ptt-90)
REVERT: A   17 LYS cc_start: 0.8931 (tptt) cc_final: 0.8684 (tppt)
REVERT: A  211 LYS cc_start: 0.8830 (mttm) cc_final: 0.8545 (mttp)
REVERT: A  229 ASP cc_start: 0.8086 (m-30) cc_final: 0.7804 (m-30)
REVERT: A  252 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6347 (t70)
REVERT: A  318 TYR cc_start: 0.7066 (t80) cc_final: 0.6856 (t80)
REVERT: A  327 GLU cc_start: 0.7774 (mp0) cc_final: 0.7513 (mp0)
REVERT: A  370 GLU cc_start: 0.8340 (pm20) cc_final: 0.7868 (pm20)
REVERT: B   61 MET cc_start: 0.8917 (ppp) cc_final: 0.8691 (ppp)
REVERT: B   68 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7103 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8883 (t80) cc_final: 0.8676 (t80)
REVERT: B  132 ASN cc_start: 0.7796 (m-40) cc_final: 0.6985 (p0)
REVERT: B  205 ASP cc_start: 0.8364 (p0) cc_final: 0.8113 (p0)
REVERT: B  292 PHE cc_start: 0.8605 (m-80) cc_final: 0.8336 (m-80)
REVERT: B  325 MET cc_start: 0.7665 (tpp) cc_final: 0.7382 (tpp)
REVERT: E   80 TYR cc_start: 0.7946 (m-80) cc_final: 0.7443 (m-80)
REVERT: E   82 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6737 (tm-30)
REVERT: E  120 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7779 (mt0)
  outliers start: 24
  outliers final: 18
  residues processed: 185
  average time/residue: 0.2373
  time to fit residues: 57.4791
Evaluate side-chains
  165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  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 69 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 93 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0470
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.0082

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 164 HIS
F 323 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 = 0.3890 r_free = 0.3890 target = 0.152350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.114673 restraints weight = 24680.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 4.70
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.2279

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= 0.137
  Angle     :  0.552  11.705  11291  Z= 0.292
  Chirality :  0.043   0.165   1269
  Planarity :  0.004   0.043   1437
  Dihedral  :  4.839  46.029   1134
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.44 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1021
  helix:  1.38 (0.25), residues: 411
  sheet: -0.49 (0.33), residues: 229
  loop : -0.66 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.013   0.001   TYR A 253 
 ARG   0.006   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  433)
  hydrogen bonds       : angle       4.86250 ( 1245)
  SS BOND              : bond        0.00283 (    3)
  SS BOND              : angle       1.30757 (    6)
  covalent geometry    : bond        0.00296 ( 8333)
  covalent geometry    : angle       0.55116 (11285)

*********************** 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
  179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7494 (mmt90) cc_final: 0.6482 (tpm170)
REVERT: F   90 TRP cc_start: 0.8327 (t-100) cc_final: 0.8020 (t-100)
REVERT: F  225 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8461 (mt)
REVERT: F  309 ASP cc_start: 0.7546 (t70) cc_final: 0.7234 (t70)
REVERT: A   17 LYS cc_start: 0.8951 (tptt) cc_final: 0.8679 (tppt)
REVERT: A   38 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7788 (ttp-110)
REVERT: A  211 LYS cc_start: 0.8685 (mttm) cc_final: 0.8464 (mttp)
REVERT: A  229 ASP cc_start: 0.7997 (m-30) cc_final: 0.7699 (m-30)
REVERT: A  317 ARG cc_start: 0.7389 (mtp-110) cc_final: 0.7088 (ttp80)
REVERT: A  318 TYR cc_start: 0.7027 (t80) cc_final: 0.6415 (t80)
REVERT: A  327 GLU cc_start: 0.7867 (mp0) cc_final: 0.7578 (mp0)
REVERT: A  390 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8350 (tp-100)
REVERT: B   68 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7178 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8851 (t80) cc_final: 0.8505 (t80)
REVERT: B  132 ASN cc_start: 0.7682 (m-40) cc_final: 0.6869 (p0)
REVERT: B  292 PHE cc_start: 0.8600 (m-80) cc_final: 0.8278 (m-80)
REVERT: B  325 MET cc_start: 0.7733 (tpp) cc_final: 0.7307 (tpp)
REVERT: E   80 TYR cc_start: 0.7795 (m-80) cc_final: 0.7138 (m-80)
REVERT: E   82 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: E  120 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7668 (mm-40)
  outliers start: 27
  outliers final: 21
  residues processed: 168
  average time/residue: 0.2348
  time to fit residues: 51.5123
Evaluate side-chains
  168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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  213 THR
Chi-restraints excluded: chain F residue  225 ILE
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  329 ILE
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 90 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
A  23 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.149978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.112052 restraints weight = 31343.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 5.14
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8336  Z= 0.149
  Angle     :  0.552  11.528  11291  Z= 0.290
  Chirality :  0.043   0.143   1269
  Planarity :  0.004   0.059   1437
  Dihedral  :  4.649  42.745   1132
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 16.87 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1021
  helix:  1.67 (0.25), residues: 411
  sheet: -0.55 (0.32), residues: 225
  loop : -0.57 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.009   0.001   TYR A 391 
 ARG   0.009   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  433)
  hydrogen bonds       : angle       4.74227 ( 1245)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       1.18987 (    6)
  covalent geometry    : bond        0.00335 ( 8333)
  covalent geometry    : angle       0.55111 (11285)

*********************** 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
  188 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7422 (mmt90) cc_final: 0.6435 (tpm170)
REVERT: F  225 ILE cc_start: 0.8719 (mt) cc_final: 0.8488 (mt)
REVERT: F  297 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7105 (m-80)
REVERT: F  319 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7240 (m-10)
REVERT: A   17 LYS cc_start: 0.8943 (tptt) cc_final: 0.8695 (tppt)
REVERT: A  229 ASP cc_start: 0.8039 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  252 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6200 (t70)
REVERT: A  317 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7180 (ttp80)
REVERT: A  318 TYR cc_start: 0.7094 (t80) cc_final: 0.6509 (t80)
REVERT: A  327 GLU cc_start: 0.7932 (mp0) cc_final: 0.7598 (mp0)
REVERT: A  390 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8315 (tp-100)
REVERT: B   61 MET cc_start: 0.8288 (ppp) cc_final: 0.7938 (ppp)
REVERT: B  105 TYR cc_start: 0.8843 (t80) cc_final: 0.8389 (t80)
REVERT: B  132 ASN cc_start: 0.7638 (m-40) cc_final: 0.6810 (p0)
REVERT: B  292 PHE cc_start: 0.8512 (m-80) cc_final: 0.8207 (m-80)
REVERT: B  297 TRP cc_start: 0.8454 (m100) cc_final: 0.8013 (m100)
REVERT: B  325 MET cc_start: 0.7865 (tpp) cc_final: 0.7470 (tpp)
REVERT: E   80 TYR cc_start: 0.7841 (m-80) cc_final: 0.7169 (m-80)
REVERT: E   82 GLN cc_start: 0.7098 (tm-30) cc_final: 0.6728 (tm-30)
REVERT: E  120 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7672 (mm-40)
  outliers start: 38
  outliers final: 29
  residues processed: 174
  average time/residue: 0.2130
  time to fit residues: 49.8923
Evaluate side-chains
  172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
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  185 ASN
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  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  333 PHE
Chi-restraints excluded: chain A residue   40 THR
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  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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    0.3980
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.152603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.116816 restraints weight = 17746.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 3.99
r_work: 0.3304 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8336  Z= 0.119
  Angle     :  0.522  11.760  11291  Z= 0.274
  Chirality :  0.042   0.146   1269
  Planarity :  0.004   0.049   1437
  Dihedral  :  4.454  37.471   1132
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1021
  helix:  2.05 (0.25), residues: 409
  sheet: -0.43 (0.33), residues: 220
  loop : -0.62 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 169 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.011   0.001   PHE F 289 
 TYR   0.019   0.001   TYR A  37 
 ARG   0.006   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  433)
  hydrogen bonds       : angle       4.59617 ( 1245)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       0.95936 (    6)
  covalent geometry    : bond        0.00253 ( 8333)
  covalent geometry    : angle       0.52215 (11285)

*********************** 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
  191 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 155
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7525 (mmt90) cc_final: 0.6544 (tpm170)
REVERT: F  225 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8521 (mt)
REVERT: F  297 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7059 (m-80)
REVERT: F  319 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7209 (m-10)
REVERT: A   17 LYS cc_start: 0.8949 (tptt) cc_final: 0.8685 (tppt)
REVERT: A  229 ASP cc_start: 0.8197 (m-30) cc_final: 0.7864 (m-30)
REVERT: A  252 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6231 (t70)
REVERT: A  318 TYR cc_start: 0.7052 (t80) cc_final: 0.6461 (t80)
REVERT: A  327 GLU cc_start: 0.7914 (mp0) cc_final: 0.7555 (mp0)
REVERT: A  370 GLU cc_start: 0.8264 (pm20) cc_final: 0.7854 (pm20)
REVERT: A  390 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8466 (tp-100)
REVERT: B   68 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7316 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8789 (t80) cc_final: 0.8409 (t80)
REVERT: B  292 PHE cc_start: 0.8445 (m-80) cc_final: 0.8206 (m-80)
REVERT: B  297 TRP cc_start: 0.8482 (m100) cc_final: 0.7989 (m100)
REVERT: B  325 MET cc_start: 0.7723 (tpp) cc_final: 0.7353 (tpp)
REVERT: E   19 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7932 (mmm-85)
REVERT: E   82 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6922 (tm-30)
REVERT: E  120 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8006 (mm-40)
  outliers start: 36
  outliers final: 29
  residues processed: 178
  average time/residue: 0.2247
  time to fit residues: 53.0393
Evaluate side-chains
  175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
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  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  283 CYS
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  224 VAL
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
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 B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0050
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.2980
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.154400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116780 restraints weight = 28048.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 4.97
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8336  Z= 0.110
  Angle     :  0.516  11.697  11291  Z= 0.269
  Chirality :  0.041   0.149   1269
  Planarity :  0.003   0.042   1437
  Dihedral  :  4.294  32.651   1132
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.57 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1021
  helix:  2.21 (0.25), residues: 409
  sheet: -0.34 (0.33), residues: 223
  loop : -0.54 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.005   0.001   HIS F  53 
 PHE   0.014   0.001   PHE E  29 
 TYR   0.021   0.001   TYR A  37 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  433)
  hydrogen bonds       : angle       4.47918 ( 1245)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       0.83777 (    6)
  covalent geometry    : bond        0.00232 ( 8333)
  covalent geometry    : angle       0.51556 (11285)

*********************** 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
  195 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 157
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7441 (mmt90) cc_final: 0.6432 (tpm170)
REVERT: F  225 ILE cc_start: 0.8743 (mt) cc_final: 0.8509 (mt)
REVERT: F  319 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7129 (m-10)
REVERT: A  229 ASP cc_start: 0.8012 (m-30) cc_final: 0.7671 (m-30)
REVERT: A  252 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6123 (t70)
REVERT: A  318 TYR cc_start: 0.6986 (t80) cc_final: 0.6444 (t80)
REVERT: A  327 GLU cc_start: 0.7947 (mp0) cc_final: 0.7613 (mp0)
REVERT: A  370 GLU cc_start: 0.8158 (pm20) cc_final: 0.7705 (pm20)
REVERT: A  390 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8203 (tp-100)
REVERT: B   68 ARG cc_start: 0.7905 (ttt180) cc_final: 0.6934 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8729 (t80) cc_final: 0.8318 (t80)
REVERT: B  292 PHE cc_start: 0.8292 (m-80) cc_final: 0.8006 (m-80)
REVERT: B  297 TRP cc_start: 0.8325 (m100) cc_final: 0.7655 (m100)
REVERT: B  325 MET cc_start: 0.7791 (tpp) cc_final: 0.7417 (tpp)
REVERT: E   19 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7825 (mmm-85)
REVERT: E   52 SER cc_start: 0.8086 (t) cc_final: 0.7015 (m)
REVERT: E   82 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6735 (tm-30)
REVERT: E  120 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7585 (mt0)
  outliers start: 38
  outliers final: 31
  residues processed: 181
  average time/residue: 0.2134
  time to fit residues: 51.6120
Evaluate side-chains
  180 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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   75 VAL
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  213 THR
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  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  224 VAL
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   59 TYR
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 B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0370
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7060

-------------------------------------------------------------------------------
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**
** B  75 GLN ** 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 = 0.3913 r_free = 0.3913 target = 0.154176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.116848 restraints weight = 24697.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 4.68
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8336  Z= 0.114
  Angle     :  0.515  11.499  11291  Z= 0.269
  Chirality :  0.042   0.171   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.243  30.965   1132
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.80 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1021
  helix:  2.29 (0.25), residues: 409
  sheet: -0.28 (0.33), residues: 223
  loop : -0.51 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 
 PHE   0.013   0.001   PHE E  29 
 TYR   0.018   0.001   TYR A  37 
 ARG   0.007   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  433)
  hydrogen bonds       : angle       4.44599 ( 1245)
  SS BOND              : bond        0.00185 (    3)
  SS BOND              : angle       0.89977 (    6)
  covalent geometry    : bond        0.00246 ( 8333)
  covalent geometry    : angle       0.51511 (11285)

*********************** 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
  194 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 152
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7499 (mmt90) cc_final: 0.6522 (tpm170)
REVERT: F  225 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (mt)
REVERT: F  319 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7152 (m-10)
REVERT: A  229 ASP cc_start: 0.7973 (m-30) cc_final: 0.7604 (m-30)
REVERT: A  252 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6006 (t70)
REVERT: A  318 TYR cc_start: 0.7056 (t80) cc_final: 0.6449 (t80)
REVERT: A  327 GLU cc_start: 0.7994 (mp0) cc_final: 0.7656 (mp0)
REVERT: A  370 GLU cc_start: 0.8179 (pm20) cc_final: 0.7757 (pm20)
REVERT: A  390 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8209 (tp-100)
REVERT: B   68 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7275 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8723 (t80) cc_final: 0.8319 (t80)
REVERT: B  254 ASP cc_start: 0.7697 (t70) cc_final: 0.7215 (t0)
REVERT: B  292 PHE cc_start: 0.8359 (m-80) cc_final: 0.8047 (m-80)
REVERT: B  297 TRP cc_start: 0.8290 (m100) cc_final: 0.7643 (m100)
REVERT: B  325 MET cc_start: 0.7755 (tpp) cc_final: 0.7345 (tpp)
REVERT: E   19 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7813 (mmm-85)
REVERT: E   52 SER cc_start: 0.8110 (t) cc_final: 0.7037 (m)
REVERT: E  120 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7562 (mt0)
  outliers start: 42
  outliers final: 37
  residues processed: 180
  average time/residue: 0.2166
  time to fit residues: 52.8081
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  : 0.946 
-------------------------------------------------------------------------------
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   53 HIS
Chi-restraints excluded: chain F residue   75 VAL
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  283 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  224 VAL
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  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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**
** B  75 GLN ** 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 = 0.3895 r_free = 0.3895 target = 0.152501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114369 restraints weight = 31050.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 5.15
r_work (final): 0.3441
-------------------------------------------------------------------------------
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 = 0.30   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 = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8336  Z= 0.136
  Angle     :  0.537  11.581  11291  Z= 0.280
  Chirality :  0.042   0.141   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.285  31.276   1132
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 19.14 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1021
  helix:  2.31 (0.25), residues: 409
  sheet: -0.28 (0.33), residues: 223
  loop : -0.57 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.010   0.001   HIS F  53 
 PHE   0.013   0.001   PHE E  29 
 TYR   0.018   0.001   TYR A  37 
 ARG   0.007   0.000   ARG F  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  433)
  hydrogen bonds       : angle       4.48283 ( 1245)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       0.90988 (    6)
  covalent geometry    : bond        0.00305 ( 8333)
  covalent geometry    : angle       0.53639 (11285)

*********************** 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
  193 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 147
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7521 (mmt90) cc_final: 0.6497 (tpm170)
REVERT: F  225 ILE cc_start: 0.8782 (mt) cc_final: 0.8548 (mt)
REVERT: F  319 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7117 (m-10)
REVERT: A  229 ASP cc_start: 0.7977 (m-30) cc_final: 0.7610 (m-30)
REVERT: A  252 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6234 (t70)
REVERT: A  318 TYR cc_start: 0.7167 (t80) cc_final: 0.6585 (t80)
REVERT: A  327 GLU cc_start: 0.8058 (mp0) cc_final: 0.7718 (mp0)
REVERT: A  370 GLU cc_start: 0.8189 (pm20) cc_final: 0.7768 (pm20)
REVERT: A  390 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8204 (tp-100)
REVERT: B   68 ARG cc_start: 0.7961 (ttt180) cc_final: 0.6980 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8785 (t80) cc_final: 0.8366 (t80)
REVERT: B  254 ASP cc_start: 0.7755 (t70) cc_final: 0.7270 (t0)
REVERT: B  292 PHE cc_start: 0.8460 (m-80) cc_final: 0.8163 (m-80)
REVERT: B  297 TRP cc_start: 0.8309 (m100) cc_final: 0.7608 (m100)
REVERT: B  325 MET cc_start: 0.7863 (tpp) cc_final: 0.7470 (tpp)
REVERT: E   52 SER cc_start: 0.8156 (t) cc_final: 0.7069 (m)
REVERT: E  120 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7564 (mt0)
  outliers start: 46
  outliers final: 39
  residues processed: 180
  average time/residue: 0.2229
  time to fit residues: 53.6576
Evaluate side-chains
  182 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 141
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   53 HIS
Chi-restraints excluded: chain F residue   75 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  201 ILE
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  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  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  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   59 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 43 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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  75 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 = 0.3912 r_free = 0.3912 target = 0.154069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.115220 restraints weight = 38046.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 5.63
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8336  Z= 0.115
  Angle     :  0.524  11.474  11291  Z= 0.272
  Chirality :  0.042   0.143   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.257  30.359   1132
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.39 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1021
  helix:  2.36 (0.25), residues: 409
  sheet: -0.28 (0.33), residues: 224
  loop : -0.54 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 
 PHE   0.011   0.001   PHE F 289 
 TYR   0.017   0.001   TYR A  37 
 ARG   0.007   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  433)
  hydrogen bonds       : angle       4.43779 ( 1245)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       1.08868 (    6)
  covalent geometry    : bond        0.00249 ( 8333)
  covalent geometry    : angle       0.52362 (11285)

*********************** 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
  181 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7417 (mmt90) cc_final: 0.6181 (tpm170)
REVERT: F  225 ILE cc_start: 0.8774 (mt) cc_final: 0.8538 (mt)
REVERT: F  319 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7112 (m-10)
REVERT: A  229 ASP cc_start: 0.7997 (m-30) cc_final: 0.7643 (m-30)
REVERT: A  252 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6282 (t70)
REVERT: A  318 TYR cc_start: 0.7045 (t80) cc_final: 0.6479 (t80)
REVERT: A  327 GLU cc_start: 0.8029 (mp0) cc_final: 0.7712 (mp0)
REVERT: A  370 GLU cc_start: 0.8081 (pm20) cc_final: 0.7662 (pm20)
REVERT: A  390 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8210 (tp-100)
REVERT: B  105 TYR cc_start: 0.8754 (t80) cc_final: 0.8506 (t80)
REVERT: B  254 ASP cc_start: 0.7712 (t70) cc_final: 0.7228 (t0)
REVERT: B  292 PHE cc_start: 0.8435 (m-80) cc_final: 0.8120 (m-80)
REVERT: B  297 TRP cc_start: 0.8266 (m100) cc_final: 0.7580 (m100)
REVERT: B  325 MET cc_start: 0.7831 (tpp) cc_final: 0.7418 (tpp)
REVERT: E   52 SER cc_start: 0.8057 (t) cc_final: 0.7055 (m)
REVERT: E  120 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7514 (mt0)
  outliers start: 38
  outliers final: 35
  residues processed: 170
  average time/residue: 0.2041
  time to fit residues: 46.9424
Evaluate side-chains
  177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   75 VAL
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  149 THR
Chi-restraints excluded: chain F residue  201 ILE
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  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  248 VAL
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   59 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 93 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0980
   chunk 98 optimal weight:    0.0570
   chunk 84 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.2302

-------------------------------------------------------------------------------
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  75 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 = 0.3889 r_free = 0.3889 target = 0.152050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114677 restraints weight = 24578.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 4.65
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8336  Z= 0.140
  Angle     :  0.544  11.483  11291  Z= 0.283
  Chirality :  0.042   0.147   1269
  Planarity :  0.004   0.042   1437
  Dihedral  :  4.294  31.103   1132
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1021
  helix:  2.36 (0.25), residues: 409
  sheet: -0.23 (0.33), residues: 222
  loop : -0.54 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 
 PHE   0.011   0.001   PHE F 289 
 TYR   0.017   0.001   TYR A  37 
 ARG   0.007   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  433)
  hydrogen bonds       : angle       4.49846 ( 1245)
  SS BOND              : bond        0.00199 (    3)
  SS BOND              : angle       1.04667 (    6)
  covalent geometry    : bond        0.00315 ( 8333)
  covalent geometry    : angle       0.54374 (11285)

********************** 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
  182 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7537 (mmt90) cc_final: 0.6293 (tpm170)
REVERT: F  225 ILE cc_start: 0.8775 (mt) cc_final: 0.8542 (mt)
REVERT: F  319 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7115 (m-10)
REVERT: A  229 ASP cc_start: 0.7987 (m-30) cc_final: 0.7620 (m-30)
REVERT: A  252 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6263 (t70)
REVERT: A  318 TYR cc_start: 0.7205 (t80) cc_final: 0.6606 (t80)
REVERT: A  327 GLU cc_start: 0.8063 (mp0) cc_final: 0.7730 (mp0)
REVERT: A  370 GLU cc_start: 0.8237 (pm20) cc_final: 0.7744 (pm20)
REVERT: A  390 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8207 (tp-100)
REVERT: B  254 ASP cc_start: 0.7798 (t70) cc_final: 0.7304 (t0)
REVERT: B  292 PHE cc_start: 0.8497 (m-80) cc_final: 0.8178 (m-80)
REVERT: B  297 TRP cc_start: 0.8339 (m100) cc_final: 0.7633 (m100)
REVERT: B  325 MET cc_start: 0.7961 (tpp) cc_final: 0.7558 (tpp)
REVERT: E   52 SER cc_start: 0.8068 (t) cc_final: 0.7054 (m)
REVERT: E  120 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7573 (mt0)
  outliers start: 38
  outliers final: 36
  residues processed: 171
  average time/residue: 0.2130
  time to fit residues: 49.5692
Evaluate side-chains
  182 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   24 ILE
Chi-restraints excluded: chain F residue   75 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  201 ILE
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  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  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
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  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0670
   chunk 69 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.9524

-------------------------------------------------------------------------------
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**
** B  75 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 = 0.3899 r_free = 0.3899 target = 0.152928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114829 restraints weight = 30058.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 5.09
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8336  Z= 0.127
  Angle     :  0.539  11.565  11291  Z= 0.280
  Chirality :  0.042   0.137   1269
  Planarity :  0.003   0.042   1437
  Dihedral  :  4.319  30.655   1132
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 21.18 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1021
  helix:  2.38 (0.25), residues: 409
  sheet: -0.14 (0.34), residues: 211
  loop : -0.50 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.012   0.001   HIS F  53 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.017   0.001   TYR A  37 
 ARG   0.007   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03959 (  433)
  hydrogen bonds       : angle       4.46488 ( 1245)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       0.99437 (    6)
  covalent geometry    : bond        0.00281 ( 8333)
  covalent geometry    : angle       0.53896 (11285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4439.87 seconds
wall clock time: 76 minutes 55.89 seconds (4615.89 seconds total)