Starting phenix.real_space_refine
on Mon Jul 28 20:49:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x2d_32965/07_2025/7x2d_32965.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x2d_32965/07_2025/7x2d_32965.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2025/7x2d_32965.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2025/7x2d_32965.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2025/7x2d_32965.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2025/7x2d_32965.cif"
  }
  resolution = 3.3
  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=   0.135
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: 5
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5215      2.51       5
     N    1428      2.21       5
     O    1502      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8203
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 2241
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 280, 2230
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 9, 'TRANS': 270}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 280, 2230
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 9, 'TRANS': 270}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 2274
    Chain: "A"
      Number of atoms: 1883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1883
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    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: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'86W': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 7.70, per 1000 atoms: 0.94
  Number of scatterers: 8203
  At special positions: 0
  Unit cell: (78.264, 97.83, 128.266, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     F       3      9.00
     O    1502      8.00
     N    1428      7.00
     C    5215      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=2.04

  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: 2.12
  Conformation dependent library (CDL) restraints added in 1.4 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:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      44.8% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'F' and resid 20 through 51
      removed outlier: 4.205A  pdb=" N   ILE F  24 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 57
      removed outlier: 3.980A  pdb=" N   ARG F  55 " --> pdb=" O   PHE F  51 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LYS F  57 " --> pdb=" O   HIS F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 77
      removed outlier: 4.340A  pdb=" N   PHE F  62 " --> pdb=" O   VAL F  58 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL F  63 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 88
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.241A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ALA F 101 " --> pdb=" O   ASN F  97 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR F 108 " --> pdb=" O   ILE F 104 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA F 109 " --> pdb=" O   MET F 105 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN F 113 " --> pdb=" O   ALA F 109 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER F 118 " --> pdb=" O   LEU F 114 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER F 127 " --> pdb=" O   TRP F 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
      removed outlier: 3.625A  pdb=" N   MET F 135 " --> pdb=" O   TYR F 131 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 136 through 161
      removed outlier: 3.875A  pdb=" N   ILE F 157 " --> pdb=" O   LEU F 153 " (cutoff:3.500A)
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
    Processing helix  chain 'F' and resid 203 through 238
    Processing helix  chain 'F' and resid 265 through 298
      removed outlier: 4.092A  pdb=" N   PHE F 281 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL F 282 " --> pdb=" O   MET F 278 " (cutoff:3.500A)
      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: 4.798A  pdb=" N   SER F 324 " --> pdb=" O   GLY F 320 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER F 325 " --> pdb=" O   TRP F 321 " (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 39
      removed outlier: 3.714A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.562A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.575A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 254
      No H-bonds generated for 'chain 'A' and resid 252 through 254'
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 4.023A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.554A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 214
      removed outlier: 9.237A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.046A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.685A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.756A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.555A  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: 6.969A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.686A  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: 3.694A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.180A  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: 6.839A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.441A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.883A  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: 3.789A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.764A  pdb=" N   MET E  34 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   ASP E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   SER E  59 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1223 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: 2.73

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1321
        1.30 -     1.43: 2323
        1.43 -     1.57: 4663
        1.57 -     1.70: 0
        1.70 -     1.83: 74
  Bond restraints: 8381
  Sorted by residual:
  bond pdb=" C19 86W F 502 "
       pdb=" C20 86W F 502 "
    ideal  model  delta    sigma   weight residual
    1.359  1.479 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" C24 86W F 502 "
       pdb=" N23 86W F 502 "
    ideal  model  delta    sigma   weight residual
    1.372  1.465 -0.093 2.00e-02 2.50e+03 2.14e+01
  bond pdb=" C24 86W F 502 "
       pdb=" N26 86W F 502 "
    ideal  model  delta    sigma   weight residual
    1.380  1.467 -0.087 2.00e-02 2.50e+03 1.90e+01
  bond pdb=" CA  SER F 191 "
       pdb=" C   SER F 191 "
    ideal  model  delta    sigma   weight residual
    1.524  1.478  0.045 1.26e-02 6.30e+03 1.28e+01
  bond pdb=" CA  CYS F 186 "
       pdb=" C   CYS F 186 "
    ideal  model  delta    sigma   weight residual
    1.530  1.493  0.036 1.10e-02 8.26e+03 1.10e+01
  ... (remaining 8376 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 11169
        2.82 -     5.64: 170
        5.64 -     8.46: 25
        8.46 -    11.28: 2
       11.28 -    14.10: 1
  Bond angle restraints: 11367
  Sorted by residual:
  angle pdb=" N   GLU D  42 "
        pdb=" CA  GLU D  42 "
        pdb=" CB  GLU D  42 "
      ideal   model   delta    sigma   weight residual
     110.39  117.99   -7.60 1.66e+00 3.63e-01 2.09e+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  112.86    9.08 2.00e+00 2.50e-01 2.06e+01
  angle pdb=" N   ILE F 125 "
        pdb=" CA  ILE F 125 "
        pdb=" C   ILE F 125 "
      ideal   model   delta    sigma   weight residual
     113.53  109.20    4.33 9.80e-01 1.04e+00 1.95e+01
  angle pdb=" C   GLY A 353 "
        pdb=" N   ASP A 354 "
        pdb=" CA  ASP A 354 "
      ideal   model   delta    sigma   weight residual
     122.07  128.37   -6.30 1.43e+00 4.89e-01 1.94e+01
  angle pdb=" N   ASN F 185 "
        pdb=" CA  ASN F 185 "
        pdb=" C   ASN F 185 "
      ideal   model   delta    sigma   weight residual
     110.28  103.95    6.33 1.48e+00 4.57e-01 1.83e+01
  ... (remaining 11362 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4513
       17.96 -    35.91: 420
       35.91 -    53.87: 90
       53.87 -    71.82: 11
       71.82 -    89.78: 9
  Dihedral angle restraints: 5043
    sinusoidal: 2025
      harmonic: 3018
  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    4.29   88.71     1      1.00e+01 1.00e-02 9.38e+01
  dihedral pdb=" CB  CYS F  96 "
           pdb=" SG  CYS F  96 "
           pdb=" SG  CYS F 186 "
           pdb=" CB  CYS F 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.69  -80.69     1      1.00e+01 1.00e-02 8.05e+01
  dihedral pdb=" CA  PHE F 333 "
           pdb=" C   PHE F 333 "
           pdb=" N   ASN F 334 "
           pdb=" CA  ASN F 334 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.79   21.21     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5040 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 974
       0.055 -    0.111: 245
       0.111 -    0.166: 40
       0.166 -    0.221: 11
       0.221 -    0.277: 5
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" C13 CLR F 501 "
            pdb=" C12 CLR F 501 "
            pdb=" C14 CLR F 501 "
            pdb=" C17 CLR F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  GLU D  42 "
            pdb=" N   GLU D  42 "
            pdb=" C   GLU D  42 "
            pdb=" CB  GLU D  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  ARG B   8 "
            pdb=" N   ARG B   8 "
            pdb=" C   ARG B   8 "
            pdb=" CB  ARG B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F 157 "    0.081 5.00e-02 4.00e+02   1.21e-01 2.35e+01
        pdb=" N   PRO F 158 "   -0.210 5.00e-02 4.00e+02
        pdb=" CA  PRO F 158 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO F 158 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 169 "   -0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   TRP B 169 "    0.056 2.00e-02 2.50e+03
        pdb=" O   TRP B 169 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP B 170 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  28 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.81e+00
        pdb=" C   LYS A  28 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS A  28 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A  29 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 42
        2.47 -     3.08: 5614
        3.08 -     3.68: 12517
        3.68 -     4.29: 18628
        4.29 -     4.90: 31003
  Nonbonded interactions: 67804
  Sorted by model distance:
  nonbonded pdb=" F16 86W F 502 "
            pdb=" O08 86W F 502 "
     model   vdw
     1.860 2.990
  nonbonded pdb=" OG1 THR F  37 "
            pdb=" OG  SER F 325 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.079 3.040
  nonbonded pdb=" OG1 THR B 173 "
            pdb=" OE1 GLN B 175 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.164 3.120
  ... (remaining 67799 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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.630
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.070
  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:3.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
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      :  0.005   0.120   8384  Z= 0.272
  Angle     :  0.854  14.105  11373  Z= 0.475
  Chirality :  0.053   0.277   1275
  Planarity :  0.006   0.121   1440
  Dihedral  : 14.430  89.779   3076
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  0.68 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1021
  helix:  0.60 (0.25), residues: 404
  sheet: -0.57 (0.32), residues: 227
  loop : -0.97 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 281 
 HIS   0.010   0.002   HIS A 220 
 PHE   0.032   0.002   PHE B 234 
 TYR   0.021   0.002   TYR A 253 
 ARG   0.006   0.001   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12703 (  430)
  hydrogen bonds       : angle       6.04787 ( 1223)
  SS BOND              : bond        0.00942 (    3)
  SS BOND              : angle       1.66133 (    6)
  covalent geometry    : bond        0.00515 ( 8381)
  covalent geometry    : angle       0.85368 (11367)

*********************** 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
  188 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8926 (tp) cc_final: 0.8717 (tp)
REVERT: F  157 ILE cc_start: 0.8838 (mm) cc_final: 0.8562 (mt)
REVERT: A  386 MET cc_start: 0.7482 (ttp) cc_final: 0.7060 (ttm)
REVERT: D   51 LEU cc_start: 0.7813 (tp) cc_final: 0.7431 (tp)
REVERT: E   78 THR cc_start: 0.7646 (t) cc_final: 0.7315 (p)
REVERT: E  117 TYR cc_start: 0.8412 (m-80) cc_final: 0.8179 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1903
  time to fit residues: 49.7369
Evaluate side-chains
  150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  23 ASN
A 292 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.167240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.132181 restraints weight = 30565.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 8.82
r_work: 0.2975 rms_B_bonded: 6.77 restraints_weight: 2.0000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8384  Z= 0.175
  Angle     :  0.606   8.794  11373  Z= 0.327
  Chirality :  0.044   0.136   1275
  Planarity :  0.005   0.080   1440
  Dihedral  :  5.187  42.969   1216
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.34 %
    Favored  : 88.18 %
  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:  0.47 (0.25), residues: 1021
  helix:  1.42 (0.24), residues: 409
  sheet:  0.08 (0.33), residues: 218
  loop : -0.67 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.030   0.002   PHE F 141 
 TYR   0.014   0.002   TYR E  32 
 ARG   0.005   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04608 (  430)
  hydrogen bonds       : angle       4.70024 ( 1223)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       1.23313 (    6)
  covalent geometry    : bond        0.00406 ( 8381)
  covalent geometry    : angle       0.60591 (11367)

*********************** 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
  163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8704 (tp) cc_final: 0.8411 (tp)
REVERT: F  278 MET cc_start: 0.8080 (tpp) cc_final: 0.7624 (tpp)
REVERT: A  307 LYS cc_start: 0.7111 (ptpp) cc_final: 0.6396 (pttp)
REVERT: A  386 MET cc_start: 0.8667 (ttp) cc_final: 0.8453 (ttm)
REVERT: B   44 GLN cc_start: 0.8012 (pm20) cc_final: 0.7803 (tm-30)
REVERT: B  197 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7647 (mmp80)
REVERT: B  325 MET cc_start: 0.8498 (mmm) cc_final: 0.8236 (tpp)
  outliers start: 10
  outliers final: 9
  residues processed: 160
  average time/residue: 0.1890
  time to fit residues: 42.4677
Evaluate side-chains
  150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   64 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0970
   chunk 92 optimal weight:    0.0060
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0770
   chunk 84 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.3954

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 266 HIS
E  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.171569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137844 restraints weight = 32688.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 8.39
r_work: 0.3039 rms_B_bonded: 6.88 restraints_weight: 2.0000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8384  Z= 0.110
  Angle     :  0.517   7.443  11373  Z= 0.277
  Chirality :  0.041   0.131   1275
  Planarity :  0.004   0.064   1440
  Dihedral  :  4.607  37.289   1216
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.84 %
    Favored  : 85.23 %
  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:  0.90 (0.26), residues: 1021
  helix:  1.83 (0.25), residues: 422
  sheet:  0.09 (0.31), residues: 225
  loop : -0.43 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.022   0.002   PHE F 141 
 TYR   0.010   0.001   TYR F 194 
 ARG   0.005   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  430)
  hydrogen bonds       : angle       4.22968 ( 1223)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       0.80445 (    6)
  covalent geometry    : bond        0.00241 ( 8381)
  covalent geometry    : angle       0.51664 (11367)

*********************** 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
  172 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8707 (tp) cc_final: 0.8438 (tp)
REVERT: A  307 LYS cc_start: 0.7226 (ptpp) cc_final: 0.6546 (pttp)
REVERT: B   10 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6766 (tt0)
REVERT: B   37 ILE cc_start: 0.8310 (tp) cc_final: 0.7543 (pt)
REVERT: B  197 ARG cc_start: 0.7867 (mmp80) cc_final: 0.7554 (mmp80)
REVERT: B  253 PHE cc_start: 0.8810 (m-80) cc_final: 0.8544 (m-80)
REVERT: B  333 ASP cc_start: 0.8755 (p0) cc_final: 0.8461 (p0)
REVERT: D   51 LEU cc_start: 0.7833 (tp) cc_final: 0.7509 (mt)
REVERT: E   60 TYR cc_start: 0.8728 (m-80) cc_final: 0.8451 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 169
  average time/residue: 0.1906
  time to fit residues: 45.5707
Evaluate side-chains
  149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.164905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.130914 restraints weight = 32353.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 8.26
r_work: 0.2936 rms_B_bonded: 6.97 restraints_weight: 2.0000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8384  Z= 0.180
  Angle     :  0.565   7.734  11373  Z= 0.302
  Chirality :  0.043   0.135   1275
  Planarity :  0.004   0.059   1440
  Dihedral  :  4.832  42.643   1216
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.77 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1021
  helix:  2.04 (0.25), residues: 411
  sheet:  0.05 (0.32), residues: 219
  loop : -0.30 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 281 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.019   0.002   PHE F 264 
 TYR   0.011   0.002   TYR E  32 
 ARG   0.003   0.000   ARG E  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04234 (  430)
  hydrogen bonds       : angle       4.34546 ( 1223)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       1.05027 (    6)
  covalent geometry    : bond        0.00423 ( 8381)
  covalent geometry    : angle       0.56458 (11367)

*********************** 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
  156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8716 (tp) cc_final: 0.8422 (tp)
REVERT: F  333 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7369 (m-10)
REVERT: A  307 LYS cc_start: 0.7253 (ptpp) cc_final: 0.6601 (pttp)
REVERT: B  197 ARG cc_start: 0.7954 (mmp80) cc_final: 0.7604 (mmp80)
REVERT: B  253 PHE cc_start: 0.8840 (m-80) cc_final: 0.8586 (m-80)
REVERT: E   31 ASN cc_start: 0.8164 (m-40) cc_final: 0.7861 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 148
  average time/residue: 0.2315
  time to fit residues: 48.3013
Evaluate side-chains
  145 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 1.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
F  41 ASN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.166518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.132327 restraints weight = 26960.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 7.56
r_work: 0.2986 rms_B_bonded: 6.63 restraints_weight: 2.0000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8384  Z= 0.135
  Angle     :  0.514   7.124  11373  Z= 0.276
  Chirality :  0.041   0.130   1275
  Planarity :  0.004   0.054   1440
  Dihedral  :  4.710  42.507   1216
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.77 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1021
  helix:  2.16 (0.25), residues: 411
  sheet:  0.13 (0.31), residues: 219
  loop : -0.32 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 281 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.020   0.002   PHE F  29 
 TYR   0.010   0.001   TYR E  32 
 ARG   0.002   0.000   ARG E  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  430)
  hydrogen bonds       : angle       4.24250 ( 1223)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.94329 (    6)
  covalent geometry    : bond        0.00308 ( 8381)
  covalent geometry    : angle       0.51397 (11367)

*********************** 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
  154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8742 (tp) cc_final: 0.8447 (tp)
REVERT: F  278 MET cc_start: 0.7967 (mmm) cc_final: 0.7417 (tpp)
REVERT: F  333 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7441 (m-10)
REVERT: A  307 LYS cc_start: 0.7311 (ptpp) cc_final: 0.6662 (pttp)
REVERT: B  197 ARG cc_start: 0.8017 (mmp80) cc_final: 0.7615 (mmp80)
REVERT: B  253 PHE cc_start: 0.8822 (m-80) cc_final: 0.8574 (m-80)
REVERT: B  325 MET cc_start: 0.8648 (tpp) cc_final: 0.8443 (tpp)
REVERT: E   31 ASN cc_start: 0.8422 (m-40) cc_final: 0.8153 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 148
  average time/residue: 0.3730
  time to fit residues: 76.0423
Evaluate side-chains
  141 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0570
   overall best weight:    1.2902

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

Flipped N/Q/H residues before XYZ refinement:
F  41 ASN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.165865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132190 restraints weight = 37508.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 9.22
r_work: 0.2943 rms_B_bonded: 7.13 restraints_weight: 2.0000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8384  Z= 0.146
  Angle     :  0.521   6.878  11373  Z= 0.280
  Chirality :  0.042   0.132   1275
  Planarity :  0.004   0.051   1440
  Dihedral  :  4.716  44.671   1216
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.57 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1021
  helix:  2.13 (0.25), residues: 417
  sheet:  0.17 (0.32), residues: 219
  loop : -0.22 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.002   PHE F 264 
 TYR   0.011   0.001   TYR F 214 
 ARG   0.002   0.000   ARG E  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  430)
  hydrogen bonds       : angle       4.25104 ( 1223)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.95450 (    6)
  covalent geometry    : bond        0.00339 ( 8381)
  covalent geometry    : angle       0.52060 (11367)

*********************** 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
  155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8713 (tp) cc_final: 0.8406 (tp)
REVERT: F  278 MET cc_start: 0.8112 (mmm) cc_final: 0.7683 (tpp)
REVERT: F  333 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7502 (m-10)
REVERT: A  307 LYS cc_start: 0.7249 (ptpp) cc_final: 0.6664 (pttp)
REVERT: B  197 ARG cc_start: 0.8105 (mmp80) cc_final: 0.7714 (mmp80)
REVERT: B  234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7475 (t80)
REVERT: B  253 PHE cc_start: 0.8842 (m-80) cc_final: 0.8597 (m-80)
REVERT: B  325 MET cc_start: 0.8729 (tpp) cc_final: 0.8493 (tpp)
REVERT: E   31 ASN cc_start: 0.8430 (m-40) cc_final: 0.8168 (t0)
  outliers start: 25
  outliers final: 19
  residues processed: 145
  average time/residue: 0.1910
  time to fit residues: 38.5810
Evaluate side-chains
  149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  275 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0270
   chunk 68 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    0.9642

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

Flipped N/Q/H residues before XYZ refinement:
F  41 ASN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.164922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.116324 restraints weight = 31386.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 5.20
r_work: 0.3045 rms_B_bonded: 5.13 restraints_weight: 2.0000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8384  Z= 0.126
  Angle     :  0.505   6.591  11373  Z= 0.270
  Chirality :  0.041   0.128   1275
  Planarity :  0.004   0.049   1440
  Dihedral  :  4.608  43.428   1216
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.80 %
    Favored  : 80.80 %
  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:  1.30 (0.26), residues: 1021
  helix:  2.23 (0.25), residues: 417
  sheet:  0.15 (0.31), residues: 227
  loop : -0.17 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.020   0.001   PHE F  29 
 TYR   0.010   0.001   TYR F 214 
 ARG   0.002   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  430)
  hydrogen bonds       : angle       4.17691 ( 1223)
  SS BOND              : bond        0.00286 (    3)
  SS BOND              : angle       0.89259 (    6)
  covalent geometry    : bond        0.00287 ( 8381)
  covalent geometry    : angle       0.50433 (11367)

*********************** 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
  160 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8705 (tp) cc_final: 0.8414 (tp)
REVERT: F  278 MET cc_start: 0.7971 (mmm) cc_final: 0.7592 (tpp)
REVERT: F  333 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7447 (m-10)
REVERT: A  307 LYS cc_start: 0.7280 (ptpp) cc_final: 0.6660 (pttp)
REVERT: A  322 GLU cc_start: 0.8357 (mp0) cc_final: 0.8108 (mp0)
REVERT: B  197 ARG cc_start: 0.8055 (mmp80) cc_final: 0.7690 (mmp80)
REVERT: B  234 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7612 (t80)
REVERT: B  253 PHE cc_start: 0.8770 (m-80) cc_final: 0.8552 (m-80)
REVERT: B  325 MET cc_start: 0.8589 (tpp) cc_final: 0.8330 (tpp)
REVERT: E   31 ASN cc_start: 0.8356 (m-40) cc_final: 0.8117 (t0)
  outliers start: 27
  outliers final: 21
  residues processed: 150
  average time/residue: 0.2107
  time to fit residues: 43.9924
Evaluate side-chains
  153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  102 PHE
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  275 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
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 57 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 63 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 24 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.166125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.130774 restraints weight = 30718.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 8.63
r_work: 0.2965 rms_B_bonded: 6.81 restraints_weight: 2.0000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8384  Z= 0.114
  Angle     :  0.497   7.272  11373  Z= 0.266
  Chirality :  0.041   0.132   1275
  Planarity :  0.003   0.047   1440
  Dihedral  :  4.482  40.924   1216
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.91 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.27), residues: 1021
  helix:  2.30 (0.25), residues: 417
  sheet:  0.16 (0.31), residues: 233
  loop : -0.12 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE F 264 
 TYR   0.009   0.001   TYR F 214 
 ARG   0.002   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03714 (  430)
  hydrogen bonds       : angle       4.14222 ( 1223)
  SS BOND              : bond        0.00248 (    3)
  SS BOND              : angle       0.79575 (    6)
  covalent geometry    : bond        0.00257 ( 8381)
  covalent geometry    : angle       0.49633 (11367)

*********************** 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
  155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8687 (tp) cc_final: 0.8374 (tp)
REVERT: F  278 MET cc_start: 0.8022 (mmm) cc_final: 0.7629 (tpp)
REVERT: F  333 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7424 (m-10)
REVERT: A  307 LYS cc_start: 0.7270 (ptpp) cc_final: 0.6657 (pttt)
REVERT: A  322 GLU cc_start: 0.8457 (mp0) cc_final: 0.8215 (mp0)
REVERT: B  197 ARG cc_start: 0.8080 (mmp80) cc_final: 0.7736 (mmp80)
REVERT: B  234 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7579 (t80)
REVERT: B  325 MET cc_start: 0.8667 (tpp) cc_final: 0.8387 (tpp)
REVERT: E   31 ASN cc_start: 0.8416 (m-40) cc_final: 0.8199 (t0)
  outliers start: 25
  outliers final: 19
  residues processed: 147
  average time/residue: 0.2049
  time to fit residues: 41.5750
Evaluate side-chains
  150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  102 PHE
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  275 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
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 17 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 60 optimal weight:    0.4980
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.166830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.133215 restraints weight = 33404.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 9.03
r_work: 0.2966 rms_B_bonded: 7.08 restraints_weight: 2.0000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8384  Z= 0.110
  Angle     :  0.494   6.982  11373  Z= 0.264
  Chirality :  0.041   0.140   1275
  Planarity :  0.003   0.046   1440
  Dihedral  :  4.388  37.855   1216
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.25 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.27), residues: 1021
  helix:  2.36 (0.25), residues: 417
  sheet:  0.20 (0.31), residues: 233
  loop : -0.10 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.001   PHE F  29 
 TYR   0.024   0.001   TYR E  60 
 ARG   0.002   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  430)
  hydrogen bonds       : angle       4.09418 ( 1223)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.73878 (    6)
  covalent geometry    : bond        0.00245 ( 8381)
  covalent geometry    : angle       0.49375 (11367)

*********************** 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
  156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8693 (tp) cc_final: 0.8375 (tp)
REVERT: F  278 MET cc_start: 0.7980 (mmm) cc_final: 0.7530 (tpp)
REVERT: F  333 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7512 (m-10)
REVERT: A  307 LYS cc_start: 0.7274 (ptpp) cc_final: 0.6666 (pttt)
REVERT: A  322 GLU cc_start: 0.8444 (mp0) cc_final: 0.8202 (mp0)
REVERT: B  197 ARG cc_start: 0.8046 (mmp80) cc_final: 0.7637 (mmp80)
REVERT: B  234 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7592 (t80)
REVERT: B  325 MET cc_start: 0.8682 (tpp) cc_final: 0.8371 (tpp)
  outliers start: 21
  outliers final: 17
  residues processed: 149
  average time/residue: 0.2292
  time to fit residues: 46.7560
Evaluate side-chains
  151 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  102 PHE
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
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 43 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    0.2980
   chunk 51 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0770
   overall best weight:    0.6140

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.167328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.128261 restraints weight = 21536.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 6.13
r_work: 0.3067 rms_B_bonded: 5.42 restraints_weight: 2.0000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8384  Z= 0.108
  Angle     :  0.494   7.141  11373  Z= 0.265
  Chirality :  0.040   0.128   1275
  Planarity :  0.003   0.046   1440
  Dihedral  :  4.326  34.894   1216
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.59 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.27), residues: 1021
  helix:  2.40 (0.25), residues: 417
  sheet:  0.21 (0.31), residues: 233
  loop : -0.07 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.019   0.001   PHE F 264 
 TYR   0.025   0.001   TYR E  60 
 ARG   0.002   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  430)
  hydrogen bonds       : angle       4.07142 ( 1223)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.74041 (    6)
  covalent geometry    : bond        0.00241 ( 8381)
  covalent geometry    : angle       0.49337 (11367)

********************** 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
  156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8725 (tp) cc_final: 0.8422 (tp)
REVERT: F  278 MET cc_start: 0.7886 (mmm) cc_final: 0.7409 (tpp)
REVERT: F  333 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7454 (m-10)
REVERT: A  307 LYS cc_start: 0.7312 (ptpp) cc_final: 0.6733 (pttt)
REVERT: B  197 ARG cc_start: 0.7969 (mmp80) cc_final: 0.7647 (mmp80)
REVERT: B  234 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7642 (t80)
REVERT: B  325 MET cc_start: 0.8551 (tpp) cc_final: 0.8250 (tpp)
  outliers start: 22
  outliers final: 19
  residues processed: 149
  average time/residue: 0.2012
  time to fit residues: 41.3687
Evaluate side-chains
  154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  102 PHE
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  275 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    5 GLN
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B 293 ASN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.166542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.117667 restraints weight = 31593.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 5.31
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8384  Z= 0.118
  Angle     :  0.498   7.133  11373  Z= 0.266
  Chirality :  0.041   0.128   1275
  Planarity :  0.003   0.046   1440
  Dihedral  :  4.345  33.519   1216
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 16.70 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.27), residues: 1021
  helix:  2.39 (0.25), residues: 417
  sheet:  0.24 (0.31), residues: 233
  loop : -0.03 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 281 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.020   0.001   PHE F  29 
 TYR   0.024   0.001   TYR E  60 
 ARG   0.002   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  430)
  hydrogen bonds       : angle       4.08674 ( 1223)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       0.78848 (    6)
  covalent geometry    : bond        0.00266 ( 8381)
  covalent geometry    : angle       0.49744 (11367)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5180.38 seconds
wall clock time: 93 minutes 55.47 seconds (5635.47 seconds total)