Starting phenix.real_space_refine
on Fri Feb 14 20:42:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f0t_31404/02_2025/7f0t_31404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f0t_31404/02_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_31404/02_2025/7f0t_31404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f0t_31404/02_2025/7f0t_31404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f0t_31404/02_2025/7f0t_31404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f0t_31404/02_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-5592/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: 6.03, per 1000 atoms: 0.74
  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: 2.16
  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: 0.74
  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: 2.42

  Time building geometry restraints manager: 2.43 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:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.740
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.300
-------------------------------------------------------------------------------
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   8333  Z= 0.660
  Angle     :  1.015  14.375  11285  Z= 0.590
  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 

*********************** 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  : 0.864 
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: 0.2709
  time to fit residues: 65.9332
Evaluate side-chains
  152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.115296 restraints weight = 24408.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 4.62
r_work: 0.3264 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    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 = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
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   8333  Z= 0.203
  Angle     :  0.597  11.474  11285  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 

*********************** 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  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7732 (mmt90) cc_final: 0.6646 (tpm170)
REVERT: F   90 TRP cc_start: 0.8434 (t-100) cc_final: 0.8031 (t-100)
REVERT: F  190 LEU cc_start: 0.8695 (mt) cc_final: 0.8378 (mp)
REVERT: F  309 ASP cc_start: 0.7593 (t70) cc_final: 0.7309 (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: 0.8241 (ptt-90)
REVERT: A   17 LYS cc_start: 0.8933 (tptt) cc_final: 0.8685 (tppt)
REVERT: A  211 LYS cc_start: 0.8830 (mttm) cc_final: 0.8545 (mttp)
REVERT: A  229 ASP cc_start: 0.8084 (m-30) cc_final: 0.7803 (m-30)
REVERT: A  252 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6350 (t70)
REVERT: A  318 TYR cc_start: 0.7066 (t80) cc_final: 0.6856 (t80)
REVERT: A  327 GLU cc_start: 0.7770 (mp0) cc_final: 0.7509 (mp0)
REVERT: A  370 GLU cc_start: 0.8337 (pm20) cc_final: 0.7866 (pm20)
REVERT: B   61 MET cc_start: 0.8919 (ppp) cc_final: 0.8692 (ppp)
REVERT: B   68 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7101 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8882 (t80) cc_final: 0.8675 (t80)
REVERT: B  132 ASN cc_start: 0.7797 (m-40) cc_final: 0.6985 (p0)
REVERT: B  205 ASP cc_start: 0.8362 (p0) cc_final: 0.8109 (p0)
REVERT: B  292 PHE cc_start: 0.8605 (m-80) cc_final: 0.8336 (m-80)
REVERT: B  325 MET cc_start: 0.7666 (tpp) cc_final: 0.7382 (tpp)
REVERT: E   80 TYR cc_start: 0.7941 (m-80) cc_final: 0.7439 (m-80)
REVERT: E   82 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6732 (tm-30)
REVERT: E  120 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7774 (mt0)
  outliers start: 24
  outliers final: 18
  residues processed: 185
  average time/residue: 0.2419
  time to fit residues: 58.3011
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  : 0.928 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0170
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.2024

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.151152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.113219 restraints weight = 24692.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 4.72
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8333  Z= 0.209
  Angle     :  0.559  11.540  11285  Z= 0.296
  Chirality :  0.043   0.217   1269
  Planarity :  0.004   0.043   1437
  Dihedral  :  4.892  46.657   1134
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.44 %
    Favored  : 79.39 %
  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:  0.21 (0.26), residues: 1021
  helix:  1.38 (0.25), residues: 409
  sheet: -0.51 (0.33), residues: 229
  loop : -0.69 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.014   0.001   PHE F 289 
 TYR   0.014   0.001   TYR A 253 
 ARG   0.006   0.000   ARG B  42 

*********************** 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
  175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7460 (mmt90) cc_final: 0.6512 (tpm170)
REVERT: F   85 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8150 (mm-30)
REVERT: F   90 TRP cc_start: 0.8321 (t-100) cc_final: 0.8017 (t-100)
REVERT: F  225 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8437 (mt)
REVERT: F  309 ASP cc_start: 0.7534 (t70) cc_final: 0.7232 (t70)
REVERT: A   17 LYS cc_start: 0.8962 (tptt) cc_final: 0.8693 (tppt)
REVERT: A   38 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7796 (ttp-110)
REVERT: A  211 LYS cc_start: 0.8696 (mttm) cc_final: 0.8470 (mttp)
REVERT: A  229 ASP cc_start: 0.7979 (m-30) cc_final: 0.7683 (m-30)
REVERT: A  317 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7085 (ttp80)
REVERT: A  318 TYR cc_start: 0.7044 (t80) cc_final: 0.6407 (t80)
REVERT: A  327 GLU cc_start: 0.7861 (mp0) cc_final: 0.7566 (mp0)
REVERT: B   68 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7149 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8854 (t80) cc_final: 0.8497 (t80)
REVERT: B  132 ASN cc_start: 0.7702 (m-40) cc_final: 0.6876 (p0)
REVERT: B  292 PHE cc_start: 0.8606 (m-80) cc_final: 0.8291 (m-80)
REVERT: B  325 MET cc_start: 0.7740 (tpp) cc_final: 0.7331 (tpp)
REVERT: E   80 TYR cc_start: 0.7820 (m-80) cc_final: 0.7145 (m-80)
REVERT: E   82 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6659 (tm-30)
REVERT: E  120 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7652 (mm-40)
  outliers start: 28
  outliers final: 22
  residues processed: 164
  average time/residue: 0.2329
  time to fit residues: 50.3882
Evaluate side-chains
  167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  270 VAL
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:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 323 ASN
F 327 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.148602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.110706 restraints weight = 31918.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 5.17
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8333  Z= 0.238
  Angle     :  0.557  11.478  11285  Z= 0.294
  Chirality :  0.043   0.143   1269
  Planarity :  0.004   0.044   1437
  Dihedral  :  4.723  43.842   1132
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.99 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.41 (0.26), residues: 1021
  helix:  1.63 (0.25), residues: 411
  sheet: -0.57 (0.33), residues: 221
  loop : -0.60 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.010   0.001   TYR A 358 
 ARG   0.006   0.000   ARG B  42 

*********************** 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
  194 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 152
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7432 (mmt90) cc_final: 0.6447 (tpm170)
REVERT: F   85 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8146 (mm-30)
REVERT: F  225 ILE cc_start: 0.8726 (mt) cc_final: 0.8495 (mt)
REVERT: F  297 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7141 (m-80)
REVERT: F  309 ASP cc_start: 0.7496 (t70) cc_final: 0.7193 (t70)
REVERT: F  319 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7260 (m-10)
REVERT: A   17 LYS cc_start: 0.8961 (tptt) cc_final: 0.8711 (tppt)
REVERT: A  229 ASP cc_start: 0.8050 (m-30) cc_final: 0.7750 (m-30)
REVERT: A  252 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6233 (t70)
REVERT: A  317 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7203 (ttp80)
REVERT: A  318 TYR cc_start: 0.7175 (t80) cc_final: 0.6574 (t80)
REVERT: A  327 GLU cc_start: 0.7947 (mp0) cc_final: 0.7602 (mp0)
REVERT: A  370 GLU cc_start: 0.8209 (pm20) cc_final: 0.7740 (pm20)
REVERT: A  390 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8337 (tp-100)
REVERT: B   61 MET cc_start: 0.8345 (ppp) cc_final: 0.7972 (ppp)
REVERT: B   68 ARG cc_start: 0.8010 (ttt180) cc_final: 0.7315 (ttt-90)
REVERT: B  105 TYR cc_start: 0.8862 (t80) cc_final: 0.8411 (t80)
REVERT: B  132 ASN cc_start: 0.7665 (m-40) cc_final: 0.6803 (p0)
REVERT: B  292 PHE cc_start: 0.8545 (m-80) cc_final: 0.8281 (m-80)
REVERT: B  297 TRP cc_start: 0.8453 (m100) cc_final: 0.7956 (m100)
REVERT: B  325 MET cc_start: 0.7891 (tpp) cc_final: 0.7492 (tpp)
REVERT: E   80 TYR cc_start: 0.7768 (m-80) cc_final: 0.7116 (m-80)
REVERT: E   82 GLN cc_start: 0.7096 (tm-30) cc_final: 0.6729 (tm-30)
REVERT: E  120 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7681 (mm-40)
  outliers start: 42
  outliers final: 35
  residues processed: 180
  average time/residue: 0.2207
  time to fit residues: 52.8149
Evaluate side-chains
  177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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  152 VAL
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  270 VAL
Chi-restraints excluded: chain F residue  283 CYS
Chi-restraints excluded: chain F residue  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  224 VAL
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  107 CYS
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:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0970
   chunk 47 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 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 = 0.3854 r_free = 0.3854 target = 0.148598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112779 restraints weight = 17969.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 3.98
r_work: 0.3253 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8333  Z= 0.223
  Angle     :  0.545  11.568  11285  Z= 0.286
  Chirality :  0.043   0.147   1269
  Planarity :  0.004   0.044   1437
  Dihedral  :  4.613  40.515   1132
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 17.44 %
    Favored  : 77.80 %
  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:  0.56 (0.26), residues: 1021
  helix:  1.78 (0.25), residues: 411
  sheet: -0.51 (0.33), residues: 228
  loop : -0.54 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 169 
 HIS   0.006   0.001   HIS F  53 
 PHE   0.013   0.001   PHE F 289 
 TYR   0.020   0.001   TYR A  37 
 ARG   0.006   0.000   ARG B  42 

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

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 147
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7518 (mmt90) cc_final: 0.6531 (tpm170)
REVERT: F   85 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8202 (mm-30)
REVERT: F  225 ILE cc_start: 0.8758 (mt) cc_final: 0.8549 (mt)
REVERT: F  297 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7107 (m-80)
REVERT: F  319 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7252 (m-10)
REVERT: A   17 LYS cc_start: 0.8952 (tptt) cc_final: 0.8664 (tppt)
REVERT: A  229 ASP cc_start: 0.8140 (m-30) cc_final: 0.7786 (m-30)
REVERT: A  252 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6247 (t70)
REVERT: A  317 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7512 (ttp80)
REVERT: A  318 TYR cc_start: 0.7268 (t80) cc_final: 0.6669 (t80)
REVERT: A  327 GLU cc_start: 0.8001 (mp0) cc_final: 0.7641 (mp0)
REVERT: A  390 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8507 (tp-100)
REVERT: B  105 TYR cc_start: 0.8880 (t80) cc_final: 0.8465 (t80)
REVERT: B  132 ASN cc_start: 0.7645 (m-40) cc_final: 0.6773 (p0)
REVERT: B  292 PHE cc_start: 0.8576 (m-80) cc_final: 0.8365 (m-80)
REVERT: B  297 TRP cc_start: 0.8539 (m100) cc_final: 0.8008 (m100)
REVERT: B  325 MET cc_start: 0.7922 (tpp) cc_final: 0.7548 (tpp)
REVERT: E   80 TYR cc_start: 0.8034 (m-80) cc_final: 0.7352 (m-80)
REVERT: E   82 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6812 (tm-30)
REVERT: E  120 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8038 (mm-40)
  outliers start: 42
  outliers final: 36
  residues processed: 176
  average time/residue: 0.2272
  time to fit residues: 53.1869
Evaluate side-chains
  178 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
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  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  284 CYS
Chi-restraints excluded: chain F residue  297 PHE
Chi-restraints excluded: chain F residue  315 VAL
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  327 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  330 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  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  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   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue  107 CYS
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.151749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.113855 restraints weight = 28289.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 4.96
r_work (final): 0.3434
-------------------------------------------------------------------------------
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 = 0.31   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 = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8333  Z= 0.163
  Angle     :  0.525  11.839  11285  Z= 0.273
  Chirality :  0.042   0.146   1269
  Planarity :  0.004   0.049   1437
  Dihedral  :  4.411  34.801   1132
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 19.03 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1021
  helix:  2.10 (0.25), residues: 409
  sheet: -0.38 (0.33), residues: 223
  loop : -0.59 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 169 
 HIS   0.005   0.001   HIS F  53 
 PHE   0.011   0.001   PHE F 289 
 TYR   0.023   0.001   TYR A  37 
 ARG   0.013   0.000   ARG B 219 

*********************** 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
  196 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7273 (mmt90) cc_final: 0.6274 (tpm170)
REVERT: F  225 ILE cc_start: 0.8744 (mt) cc_final: 0.8496 (mt)
REVERT: F  297 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.7058 (m-80)
REVERT: F  319 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7209 (m-10)
REVERT: A  229 ASP cc_start: 0.8000 (m-30) cc_final: 0.7659 (m-30)
REVERT: A  252 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6093 (t70)
REVERT: A  318 TYR cc_start: 0.7083 (t80) cc_final: 0.6550 (t80)
REVERT: A  327 GLU cc_start: 0.7999 (mp0) cc_final: 0.7646 (mp0)
REVERT: A  358 TYR cc_start: 0.8405 (m-80) cc_final: 0.8145 (m-10)
REVERT: A  370 GLU cc_start: 0.8153 (pm20) cc_final: 0.7702 (pm20)
REVERT: A  390 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8244 (tp-100)
REVERT: B  105 TYR cc_start: 0.8806 (t80) cc_final: 0.8374 (t80)
REVERT: B  254 ASP cc_start: 0.7704 (t70) cc_final: 0.7183 (t0)
REVERT: B  292 PHE cc_start: 0.8411 (m-80) cc_final: 0.8119 (m-80)
REVERT: B  297 TRP cc_start: 0.8365 (m100) cc_final: 0.7966 (m100)
REVERT: B  325 MET cc_start: 0.7804 (tpp) cc_final: 0.7365 (tpp)
REVERT: E   19 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7896 (mmm-85)
REVERT: E   52 SER cc_start: 0.8203 (t) cc_final: 0.8002 (t)
REVERT: E  120 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7658 (mm-40)
  outliers start: 38
  outliers final: 30
  residues processed: 183
  average time/residue: 0.2174
  time to fit residues: 53.0731
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  : 0.923 
-------------------------------------------------------------------------------
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  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  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  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  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  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:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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  88 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.151743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114376 restraints weight = 24844.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 4.67
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8333  Z= 0.177
  Angle     :  0.531  11.550  11285  Z= 0.275
  Chirality :  0.042   0.145   1269
  Planarity :  0.004   0.050   1437
  Dihedral  :  4.342  32.218   1132
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.48 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1021
  helix:  2.17 (0.25), residues: 410
  sheet: -0.37 (0.33), residues: 223
  loop : -0.53 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.010   0.001   HIS F  53 
 PHE   0.014   0.001   PHE E  29 
 TYR   0.020   0.001   TYR A  37 
 ARG   0.010   0.000   ARG B 219 

*********************** 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
  190 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7270 (mmt90) cc_final: 0.6317 (tpm170)
REVERT: F  225 ILE cc_start: 0.8761 (mt) cc_final: 0.8521 (mt)
REVERT: F  319 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7183 (m-10)
REVERT: A  229 ASP cc_start: 0.7976 (m-30) cc_final: 0.7604 (m-30)
REVERT: A  252 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6259 (t70)
REVERT: A  283 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7776 (ttp80)
REVERT: A  318 TYR cc_start: 0.7106 (t80) cc_final: 0.6653 (t80)
REVERT: A  327 GLU cc_start: 0.8043 (mp0) cc_final: 0.7688 (mp0)
REVERT: A  358 TYR cc_start: 0.8379 (m-80) cc_final: 0.8119 (m-10)
REVERT: A  370 GLU cc_start: 0.8170 (pm20) cc_final: 0.7723 (pm20)
REVERT: A  390 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8229 (tp-100)
REVERT: B  105 TYR cc_start: 0.8795 (t80) cc_final: 0.8369 (t80)
REVERT: B  254 ASP cc_start: 0.7732 (t70) cc_final: 0.7188 (t0)
REVERT: B  292 PHE cc_start: 0.8419 (m-80) cc_final: 0.8139 (m-80)
REVERT: B  297 TRP cc_start: 0.8372 (m100) cc_final: 0.8004 (m100)
REVERT: B  325 MET cc_start: 0.7899 (tpp) cc_final: 0.7454 (tpp)
REVERT: E   19 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7877 (mmm-85)
REVERT: E   52 SER cc_start: 0.8191 (t) cc_final: 0.7990 (t)
REVERT: E   73 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7240 (t70)
REVERT: E  120 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7575 (mt0)
  outliers start: 44
  outliers final: 37
  residues processed: 177
  average time/residue: 0.2050
  time to fit residues: 49.3329
Evaluate side-chains
  179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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   78 MET
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  161 LEU
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  283 CYS
Chi-restraints excluded: chain F residue  284 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   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  226 GLU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   73 ASP
Chi-restraints excluded: chain E residue  125 THR
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:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0980
   chunk 77 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    0.7784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.152324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.114380 restraints weight = 31103.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 5.13
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3441
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    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 = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8333  Z= 0.168
  Angle     :  0.532  11.434  11285  Z= 0.274
  Chirality :  0.042   0.193   1269
  Planarity :  0.004   0.047   1437
  Dihedral  :  4.300  30.994   1132
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 20.05 %
    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:  0.93 (0.26), residues: 1021
  helix:  2.25 (0.25), residues: 409
  sheet: -0.36 (0.33), residues: 223
  loop : -0.52 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS F  53 
 PHE   0.013   0.001   PHE E  29 
 TYR   0.019   0.001   TYR A  37 
 ARG   0.010   0.000   ARG B 219 

*********************** 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
  192 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 148
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7547 (mmt90) cc_final: 0.6395 (tpm170)
REVERT: F  225 ILE cc_start: 0.8763 (mt) cc_final: 0.8522 (mt)
REVERT: F  319 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7109 (m-10)
REVERT: A  229 ASP cc_start: 0.8004 (m-30) cc_final: 0.7638 (m-30)
REVERT: A  252 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6286 (t70)
REVERT: A  318 TYR cc_start: 0.7074 (t80) cc_final: 0.6623 (t80)
REVERT: A  327 GLU cc_start: 0.8084 (mp0) cc_final: 0.7729 (mp0)
REVERT: A  370 GLU cc_start: 0.8185 (pm20) cc_final: 0.7738 (pm20)
REVERT: A  390 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8207 (tp-100)
REVERT: B  105 TYR cc_start: 0.8783 (t80) cc_final: 0.8578 (t80)
REVERT: B  254 ASP cc_start: 0.7704 (t70) cc_final: 0.7160 (t0)
REVERT: B  292 PHE cc_start: 0.8429 (m-80) cc_final: 0.8147 (m-80)
REVERT: B  297 TRP cc_start: 0.8297 (m100) cc_final: 0.7857 (m100)
REVERT: B  325 MET cc_start: 0.7997 (tpp) cc_final: 0.7548 (tpp)
REVERT: E   19 ARG cc_start: 0.8130 (ttt-90) cc_final: 0.7869 (mmm-85)
REVERT: E   52 SER cc_start: 0.8134 (t) cc_final: 0.7028 (m)
REVERT: E   53 GLN cc_start: 0.7775 (mp10) cc_final: 0.7009 (mm-40)
REVERT: E   73 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7241 (t70)
REVERT: E  120 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7495 (mt0)
  outliers start: 44
  outliers final: 38
  residues processed: 179
  average time/residue: 0.2124
  time to fit residues: 51.1814
Evaluate side-chains
  184 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 143
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  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  161 LEU
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  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  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   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   73 ASP
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:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.150753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111812 restraints weight = 38455.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 5.58
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8333  Z= 0.262
  Angle     :  0.565  11.467  11285  Z= 0.295
  Chirality :  0.043   0.137   1269
  Planarity :  0.004   0.046   1437
  Dihedral  :  4.439  32.798   1132
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 20.84 %
    Favored  : 74.18 %
  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:  0.87 (0.26), residues: 1021
  helix:  2.23 (0.25), residues: 401
  sheet: -0.42 (0.33), residues: 223
  loop : -0.50 (0.31), residues: 397

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 B 199 
 TYR   0.018   0.002   TYR A  37 
 ARG   0.009   0.000   ARG F  52 

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

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 145
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7523 (mmt90) cc_final: 0.6253 (tpm170)
REVERT: F  225 ILE cc_start: 0.8778 (mt) cc_final: 0.8547 (mt)
REVERT: F  319 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7222 (m-10)
REVERT: A  229 ASP cc_start: 0.7973 (m-30) cc_final: 0.7604 (m-30)
REVERT: A  252 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6280 (t70)
REVERT: A  318 TYR cc_start: 0.7280 (t80) cc_final: 0.6805 (t80)
REVERT: A  327 GLU cc_start: 0.8155 (mp0) cc_final: 0.7791 (mp0)
REVERT: A  358 TYR cc_start: 0.8408 (m-80) cc_final: 0.8147 (m-10)
REVERT: A  370 GLU cc_start: 0.8293 (pm20) cc_final: 0.7871 (pm20)
REVERT: A  390 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8251 (tp-100)
REVERT: B  124 TYR cc_start: 0.8009 (m-80) cc_final: 0.7499 (m-80)
REVERT: B  134 ARG cc_start: 0.6848 (ptt90) cc_final: 0.5488 (mtm-85)
REVERT: B  254 ASP cc_start: 0.7762 (t70) cc_final: 0.7247 (t0)
REVERT: B  292 PHE cc_start: 0.8552 (m-80) cc_final: 0.8247 (m-80)
REVERT: B  297 TRP cc_start: 0.8361 (m100) cc_final: 0.7944 (m100)
REVERT: B  325 MET cc_start: 0.8067 (tpp) cc_final: 0.7584 (tpp)
REVERT: E   52 SER cc_start: 0.8259 (t) cc_final: 0.7138 (m)
REVERT: E   53 GLN cc_start: 0.7869 (mp10) cc_final: 0.7085 (mm-40)
REVERT: E  120 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7591 (mt0)
  outliers start: 44
  outliers final: 40
  residues processed: 177
  average time/residue: 0.2119
  time to fit residues: 50.6885
Evaluate side-chains
  186 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 144
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
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   48 VAL
Chi-restraints excluded: chain F residue   53 HIS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  136 THR
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  149 THR
Chi-restraints excluded: chain F residue  161 LEU
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  284 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   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   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:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0060
   chunk 98 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.1402

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.111489 restraints weight = 24992.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 4.60
r_work: 0.3200 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8333  Z= 0.302
  Angle     :  0.585  11.570  11285  Z= 0.306
  Chirality :  0.044   0.139   1269
  Planarity :  0.004   0.047   1437
  Dihedral  :  4.593  34.233   1132
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 21.18 %
    Favored  : 74.07 %
  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:  0.77 (0.26), residues: 1021
  helix:  2.11 (0.25), residues: 404
  sheet: -0.63 (0.33), residues: 221
  loop : -0.42 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.008   0.001   HIS F  53 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.019   0.002   TYR A  37 
 ARG   0.008   0.000   ARG B 219 

********************** 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
  185 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 143
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.7634 (mmt90) cc_final: 0.6419 (tpm170)
REVERT: F  225 ILE cc_start: 0.8770 (mt) cc_final: 0.8558 (mt)
REVERT: F  319 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7214 (m-10)
REVERT: A  229 ASP cc_start: 0.8045 (m-30) cc_final: 0.7719 (m-30)
REVERT: A  252 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6316 (t70)
REVERT: A  318 TYR cc_start: 0.7284 (t80) cc_final: 0.6801 (t80)
REVERT: A  327 GLU cc_start: 0.8150 (mp0) cc_final: 0.7767 (mp0)
REVERT: A  370 GLU cc_start: 0.8356 (pm20) cc_final: 0.7972 (pm20)
REVERT: A  390 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8499 (tp-100)
REVERT: B  134 ARG cc_start: 0.6957 (ptt90) cc_final: 0.5781 (mtm-85)
REVERT: B  212 ASP cc_start: 0.7984 (t0) cc_final: 0.7399 (t0)
REVERT: B  254 ASP cc_start: 0.8029 (t70) cc_final: 0.7576 (t0)
REVERT: B  292 PHE cc_start: 0.8623 (m-80) cc_final: 0.8350 (m-80)
REVERT: B  297 TRP cc_start: 0.8515 (m100) cc_final: 0.8009 (m100)
REVERT: B  325 MET cc_start: 0.8078 (tpp) cc_final: 0.7660 (tpp)
REVERT: E   52 SER cc_start: 0.8171 (t) cc_final: 0.7899 (t)
REVERT: E   53 GLN cc_start: 0.7728 (mp10) cc_final: 0.7146 (mm-40)
REVERT: E  120 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8001 (mt0)
  outliers start: 42
  outliers final: 39
  residues processed: 171
  average time/residue: 0.2143
  time to fit residues: 48.9745
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  : 0.940 
-------------------------------------------------------------------------------
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   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  161 LEU
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  284 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   40 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   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:    0.7980
   chunk 62 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0270
   chunk 69 optimal weight:    0.0470
   chunk 30 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 84 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.153881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115746 restraints weight = 30062.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 5.11
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8333  Z= 0.150
  Angle     :  0.531  11.956  11285  Z= 0.276
  Chirality :  0.042   0.140   1269
  Planarity :  0.004   0.043   1437
  Dihedral  :  4.352  29.514   1132
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.10 %
    Favored  : 73.50 %
  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:  0.96 (0.27), residues: 1021
  helix:  2.33 (0.25), residues: 409
  sheet: -0.57 (0.33), residues: 224
  loop : -0.40 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.011   0.001   HIS F  53 
 PHE   0.012   0.001   PHE E  29 
 TYR   0.019   0.001   TYR A  37 
 ARG   0.009   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4230.75 seconds
wall clock time: 75 minutes 43.78 seconds (4543.78 seconds total)