Starting phenix.real_space_refine
on Wed Feb  4 12:11:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x2d_32965/02_2026/7x2d_32965.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x2d_32965/02_2026/7x2d_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x2d_32965/02_2026/7x2d_32965.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x2d_32965/02_2026/7x2d_32965.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x2d_32965/02_2026/7x2d_32965.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x2d_32965/02_2026/7x2d_32965.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.135
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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, 'ARG:plan': 1, 'GLU: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: 2.21, per 1000 atoms: 0.27
  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: 0.63
  Conformation dependent library (CDL) restraints added in 369.8 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  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: 0.21
  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: 1.09

  Time building geometry restraints manager: 0.79 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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.490
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.130
-------------------------------------------------------------------------------
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 : 12.08
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (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
 ARG   0.006   0.001   ARG A 333 
 TYR   0.021   0.002   TYR A 253 
 PHE   0.032   0.002   PHE B 234 
 TRP   0.027   0.002   TRP A 281 
 HIS   0.010   0.002   HIS A 220 

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

*********************** 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  : 0.273 
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: 0.8718 (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: 0.7432 (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: 0.0735
  time to fit residues: 19.5140
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  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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
B  88 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.170122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135213 restraints weight = 33204.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 9.23
r_work: 0.3017 rms_B_bonded: 7.39 restraints_weight: 2.0000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8384  Z= 0.141
  Angle     :  0.576   8.173  11373  Z= 0.311
  Chirality :  0.043   0.136   1275
  Planarity :  0.005   0.078   1440
  Dihedral  :  5.010  38.718   1216
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.11 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.25), residues: 1021
  helix:  1.52 (0.25), residues: 409
  sheet:  0.03 (0.32), residues: 220
  loop : -0.66 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 333 
 TYR   0.012   0.001   TYR E  32 
 PHE   0.030   0.002   PHE F 141 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8381)
  covalent geometry    : angle       0.57550 (11367)
  SS BOND              : bond        0.00301 (    3)
  SS BOND              : angle       1.05251 (    6)
  hydrogen bonds       : bond        0.04386 (  430)
  hydrogen bonds       : angle       4.63684 ( 1223)

*********************** 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: 8
    poor density    : 155
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8738 (tp) cc_final: 0.8456 (tp)
REVERT: A  307 LYS cc_start: 0.7042 (ptpp) cc_final: 0.6361 (pttp)
REVERT: B   44 GLN cc_start: 0.8031 (pm20) cc_final: 0.7816 (tm-30)
REVERT: B  197 ARG cc_start: 0.7928 (mmp80) cc_final: 0.7605 (mmp80)
REVERT: B  325 MET cc_start: 0.8483 (mmm) cc_final: 0.8245 (tpp)
REVERT: B  333 ASP cc_start: 0.8804 (p0) cc_final: 0.8447 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 160
  average time/residue: 0.0683
  time to fit residues: 15.5677
Evaluate side-chains
  147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 39 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
E   3 GLN
E   5 GLN
E  31 ASN
E 123 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.166526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130342 restraints weight = 27844.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 8.03
r_work: 0.2994 rms_B_bonded: 6.25 restraints_weight: 2.0000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8384  Z= 0.164
  Angle     :  0.562   8.097  11373  Z= 0.302
  Chirality :  0.042   0.132   1275
  Planarity :  0.004   0.065   1440
  Dihedral  :  4.875  41.884   1216
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.93 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1021
  helix:  1.71 (0.25), residues: 423
  sheet:  0.12 (0.31), residues: 223
  loop : -0.48 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 283 
 TYR   0.015   0.001   TYR B 105 
 PHE   0.020   0.002   PHE F  29 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8381)
  covalent geometry    : angle       0.56209 (11367)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       1.02264 (    6)
  hydrogen bonds       : bond        0.04277 (  430)
  hydrogen bonds       : angle       4.38360 ( 1223)

*********************** 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
  165 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8741 (tp) cc_final: 0.8458 (tp)
REVERT: F  278 MET cc_start: 0.7983 (mmm) cc_final: 0.7554 (tpp)
REVERT: A  307 LYS cc_start: 0.7268 (ptpp) cc_final: 0.6589 (pttp)
REVERT: B   37 ILE cc_start: 0.8299 (tp) cc_final: 0.7531 (pt)
REVERT: B  197 ARG cc_start: 0.7921 (mmp80) cc_final: 0.7573 (mmp80)
REVERT: B  253 PHE cc_start: 0.8858 (m-80) cc_final: 0.8648 (m-80)
REVERT: E    5 GLN cc_start: 0.5697 (OUTLIER) cc_final: 0.5280 (mp10)
  outliers start: 21
  outliers final: 15
  residues processed: 158
  average time/residue: 0.0687
  time to fit residues: 15.1656
Evaluate side-chains
  152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
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  275 SER
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  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue    5 GLN
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 11 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 28 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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
E   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.165999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.131713 restraints weight = 33916.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 8.57
r_work: 0.2948 rms_B_bonded: 6.84 restraints_weight: 2.0000
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8384  Z= 0.156
  Angle     :  0.538   7.675  11373  Z= 0.290
  Chirality :  0.042   0.132   1275
  Planarity :  0.004   0.057   1440
  Dihedral  :  4.852  43.529   1216
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.07 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.26), residues: 1021
  helix:  1.83 (0.25), residues: 423
  sheet: -0.02 (0.31), residues: 229
  loop : -0.33 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.017   0.001   TYR B 105 
 PHE   0.019   0.002   PHE F 264 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8381)
  covalent geometry    : angle       0.53728 (11367)
  SS BOND              : bond        0.00303 (    3)
  SS BOND              : angle       1.01250 (    6)
  hydrogen bonds       : bond        0.04162 (  430)
  hydrogen bonds       : angle       4.33818 ( 1223)

*********************** 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
  163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8715 (tp) cc_final: 0.8423 (tp)
REVERT: F  278 MET cc_start: 0.8040 (mmm) cc_final: 0.7669 (tpp)
REVERT: F  333 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7314 (m-10)
REVERT: A  307 LYS cc_start: 0.7263 (ptpp) cc_final: 0.6575 (pttp)
REVERT: B   37 ILE cc_start: 0.8240 (tp) cc_final: 0.7541 (pt)
REVERT: B  197 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7604 (mmp80)
REVERT: B  220 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7038 (mt0)
REVERT: D   48 ASP cc_start: 0.8693 (t0) cc_final: 0.8489 (t0)
REVERT: D   51 LEU cc_start: 0.7923 (tp) cc_final: 0.7592 (mt)
  outliers start: 26
  outliers final: 18
  residues processed: 153
  average time/residue: 0.0718
  time to fit residues: 15.5268
Evaluate side-chains
  152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  248 VAL
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  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   64 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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
E   3 GLN
E  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.166402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.130155 restraints weight = 24544.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 7.45
r_work: 0.3010 rms_B_bonded: 6.27 restraints_weight: 2.0000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2277

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     :  0.513   7.138  11373  Z= 0.275
  Chirality :  0.041   0.134   1275
  Planarity :  0.004   0.053   1440
  Dihedral  :  4.703  43.839   1216
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.09 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1021
  helix:  2.18 (0.25), residues: 411
  sheet:  0.13 (0.31), residues: 219
  loop : -0.28 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.012   0.001   TYR B 105 
 PHE   0.021   0.002   PHE F  29 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8381)
  covalent geometry    : angle       0.51243 (11367)
  SS BOND              : bond        0.00269 (    3)
  SS BOND              : angle       0.85431 (    6)
  hydrogen bonds       : bond        0.03943 (  430)
  hydrogen bonds       : angle       4.22007 ( 1223)

*********************** 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
  158 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8748 (tp) cc_final: 0.8461 (tp)
REVERT: F  278 MET cc_start: 0.8011 (mmm) cc_final: 0.7678 (tpp)
REVERT: F  333 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7536 (m-10)
REVERT: A  307 LYS cc_start: 0.7309 (ptpp) cc_final: 0.6668 (pttp)
REVERT: B  197 ARG cc_start: 0.7994 (mmp80) cc_final: 0.7599 (mmp80)
REVERT: B  253 PHE cc_start: 0.8766 (m-80) cc_final: 0.8531 (m-80)
REVERT: B  325 MET cc_start: 0.8654 (tpp) cc_final: 0.8436 (tpp)
  outliers start: 24
  outliers final: 18
  residues processed: 152
  average time/residue: 0.0631
  time to fit residues: 13.7414
Evaluate side-chains
  147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  248 VAL
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  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   64 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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
E   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.117485 restraints weight = 43340.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 5.15
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2392

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= 0.133
  Angle     :  0.516   6.686  11373  Z= 0.276
  Chirality :  0.042   0.170   1275
  Planarity :  0.004   0.050   1440
  Dihedral  :  4.675  43.885   1216
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.89 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.26), residues: 1021
  helix:  2.23 (0.25), residues: 411
  sheet:  0.27 (0.31), residues: 218
  loop : -0.29 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  38 
 TYR   0.010   0.001   TYR F 214 
 PHE   0.018   0.001   PHE F 264 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8381)
  covalent geometry    : angle       0.51593 (11367)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.91386 (    6)
  hydrogen bonds       : bond        0.03924 (  430)
  hydrogen bonds       : angle       4.19370 ( 1223)

*********************** 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
  153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8811 (tp) cc_final: 0.8566 (tp)
REVERT: F  278 MET cc_start: 0.7739 (mmm) cc_final: 0.7453 (tpp)
REVERT: F  333 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7446 (m-10)
REVERT: A  307 LYS cc_start: 0.7333 (ptpp) cc_final: 0.6704 (pttp)
REVERT: B  197 ARG cc_start: 0.7765 (mmp80) cc_final: 0.7421 (mmp80)
REVERT: B  220 GLN cc_start: 0.7949 (mt0) cc_final: 0.7375 (mt0)
REVERT: B  325 MET cc_start: 0.7976 (tpp) cc_final: 0.7766 (tpp)
  outliers start: 23
  outliers final: 16
  residues processed: 146
  average time/residue: 0.0752
  time to fit residues: 15.3804
Evaluate side-chains
  142 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  248 VAL
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  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   64 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 98 optimal weight:    0.0970
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
E   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.168014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.132842 restraints weight = 31107.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 8.72
r_work: 0.3010 rms_B_bonded: 6.68 restraints_weight: 2.0000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8384  Z= 0.116
  Angle     :  0.501   6.604  11373  Z= 0.267
  Chirality :  0.041   0.142   1275
  Planarity :  0.003   0.047   1440
  Dihedral  :  4.533  40.978   1216
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.25 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.27), residues: 1021
  helix:  2.30 (0.25), residues: 417
  sheet:  0.30 (0.31), residues: 228
  loop : -0.14 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  38 
 TYR   0.010   0.001   TYR F 214 
 PHE   0.021   0.001   PHE F  29 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8381)
  covalent geometry    : angle       0.50054 (11367)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.79088 (    6)
  hydrogen bonds       : bond        0.03749 (  430)
  hydrogen bonds       : angle       4.08452 ( 1223)

*********************** 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
  149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8738 (tp) cc_final: 0.8444 (tp)
REVERT: F  333 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7504 (m-10)
REVERT: A  307 LYS cc_start: 0.7270 (ptpp) cc_final: 0.6624 (pttp)
REVERT: B  197 ARG cc_start: 0.7936 (mmp80) cc_final: 0.7609 (mmp80)
REVERT: B  220 GLN cc_start: 0.7921 (mt0) cc_final: 0.7361 (mt0)
REVERT: B  234 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7515 (t80)
REVERT: B  253 PHE cc_start: 0.8764 (m-80) cc_final: 0.8479 (m-80)
REVERT: B  325 MET cc_start: 0.8601 (tpp) cc_final: 0.8304 (tpp)
REVERT: E  120 GLN cc_start: 0.7482 (mp10) cc_final: 0.7279 (mp10)
  outliers start: 17
  outliers final: 12
  residues processed: 143
  average time/residue: 0.0722
  time to fit residues: 14.4640
Evaluate side-chains
  146 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  275 SER
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain F residue  344 LEU
Chi-restraints excluded: chain A residue  248 VAL
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  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.5782

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.163196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.114542 restraints weight = 26603.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 4.70
r_work: 0.3041 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8384  Z= 0.165
  Angle     :  0.536   7.213  11373  Z= 0.286
  Chirality :  0.042   0.145   1275
  Planarity :  0.004   0.047   1440
  Dihedral  :  4.690  44.834   1216
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.02 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.26), residues: 1021
  helix:  2.26 (0.25), residues: 411
  sheet:  0.35 (0.32), residues: 202
  loop : -0.17 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  67 
 TYR   0.021   0.002   TYR E  60 
 PHE   0.018   0.002   PHE F 264 
 TRP   0.013   0.002   TRP A 281 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8381)
  covalent geometry    : angle       0.53553 (11367)
  SS BOND              : bond        0.00294 (    3)
  SS BOND              : angle       0.91907 (    6)
  hydrogen bonds       : bond        0.04037 (  430)
  hydrogen bonds       : angle       4.26523 ( 1223)

*********************** 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
  153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8724 (tp) cc_final: 0.8448 (tp)
REVERT: F  333 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7373 (m-10)
REVERT: A   61 ARG cc_start: 0.6407 (mtm110) cc_final: 0.6103 (mtm110)
REVERT: A  307 LYS cc_start: 0.7266 (ptpp) cc_final: 0.6631 (pttp)
REVERT: B  197 ARG cc_start: 0.7992 (mmp80) cc_final: 0.7639 (mmp80)
REVERT: B  220 GLN cc_start: 0.7863 (mt0) cc_final: 0.7344 (mt0)
REVERT: B  234 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7543 (t80)
REVERT: E  120 GLN cc_start: 0.7450 (mp10) cc_final: 0.7248 (mp10)
  outliers start: 22
  outliers final: 15
  residues processed: 146
  average time/residue: 0.0686
  time to fit residues: 14.0063
Evaluate side-chains
  147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  248 VAL
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  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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
E   5 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.165484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.120360 restraints weight = 33654.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 4.96
r_work: 0.3068 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    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 = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8384  Z= 0.119
  Angle     :  0.504   6.898  11373  Z= 0.269
  Chirality :  0.041   0.136   1275
  Planarity :  0.004   0.046   1440
  Dihedral  :  4.578  44.749   1216
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.93 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.26), residues: 1021
  helix:  2.24 (0.25), residues: 417
  sheet:  0.35 (0.32), residues: 204
  loop : -0.19 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  38 
 TYR   0.022   0.001   TYR E  60 
 PHE   0.021   0.001   PHE F  29 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8381)
  covalent geometry    : angle       0.50404 (11367)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       0.83070 (    6)
  hydrogen bonds       : bond        0.03802 (  430)
  hydrogen bonds       : angle       4.15660 ( 1223)

*********************** 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
  150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8746 (tp) cc_final: 0.8451 (tp)
REVERT: F  333 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7438 (m-10)
REVERT: A   61 ARG cc_start: 0.6432 (mtm110) cc_final: 0.6149 (mtm110)
REVERT: A  307 LYS cc_start: 0.7285 (ptpp) cc_final: 0.6715 (pttt)
REVERT: B  197 ARG cc_start: 0.7990 (mmp80) cc_final: 0.7666 (mmp80)
REVERT: B  220 GLN cc_start: 0.7840 (mt0) cc_final: 0.7387 (mt0)
REVERT: B  234 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7690 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 144
  average time/residue: 0.0686
  time to fit residues: 13.6184
Evaluate side-chains
  146 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
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  248 VAL
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  105 TYR
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   49 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:   20.0000
   chunk 99 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** F  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3818 r_free = 0.3818 target = 0.163373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.118779 restraints weight = 37161.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 5.67
r_work: 0.3010 rms_B_bonded: 5.34 restraints_weight: 2.0000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8384  Z= 0.159
  Angle     :  0.540   9.346  11373  Z= 0.286
  Chirality :  0.042   0.139   1275
  Planarity :  0.004   0.046   1440
  Dihedral  :  4.667  46.108   1216
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.25 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.26), residues: 1021
  helix:  2.14 (0.25), residues: 421
  sheet:  0.29 (0.33), residues: 204
  loop : -0.20 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  67 
 TYR   0.023   0.002   TYR E  60 
 PHE   0.019   0.002   PHE F 264 
 TRP   0.016   0.002   TRP A 281 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8381)
  covalent geometry    : angle       0.53974 (11367)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       0.92324 (    6)
  hydrogen bonds       : bond        0.04008 (  430)
  hydrogen bonds       : angle       4.25138 ( 1223)

********************** 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
  153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  154 ILE cc_start: 0.8755 (tp) cc_final: 0.8470 (tp)
REVERT: F  333 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7374 (m-10)
REVERT: A   61 ARG cc_start: 0.6353 (mtm110) cc_final: 0.6105 (mtm110)
REVERT: A  307 LYS cc_start: 0.7294 (ptpp) cc_final: 0.6718 (pttt)
REVERT: B  197 ARG cc_start: 0.8032 (mmp80) cc_final: 0.7665 (mmp80)
REVERT: B  220 GLN cc_start: 0.7897 (mt0) cc_final: 0.7377 (mt0)
REVERT: B  234 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7649 (t80)
REVERT: E   90 ASP cc_start: 0.7903 (m-30) cc_final: 0.7603 (m-30)
  outliers start: 22
  outliers final: 18
  residues processed: 146
  average time/residue: 0.0646
  time to fit residues: 13.1532
Evaluate side-chains
  152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  248 VAL
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  105 TYR
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   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 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 88 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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
E   5 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.166628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.118306 restraints weight = 31671.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 5.30
r_work: 0.3048 rms_B_bonded: 5.13 restraints_weight: 2.0000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    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 = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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   0.036   8384  Z= 0.112
  Angle     :  0.506   9.293  11373  Z= 0.269
  Chirality :  0.041   0.133   1275
  Planarity :  0.003   0.045   1440
  Dihedral  :  4.512  42.347   1216
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.27), residues: 1021
  helix:  2.29 (0.25), residues: 417
  sheet:  0.33 (0.32), residues: 204
  loop : -0.14 (0.32), residues: 400

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8381)
  covalent geometry    : angle       0.50629 (11367)
  SS BOND              : bond        0.00227 (    3)
  SS BOND              : angle       0.78925 (    6)
  hydrogen bonds       : bond        0.03724 (  430)
  hydrogen bonds       : angle       4.13842 ( 1223)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1791.02 seconds
wall clock time: 31 minutes 17.03 seconds (1877.03 seconds total)