Starting phenix.real_space_refine
on Sun Apr  5 11:59:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xbj_22117/04_2026/6xbj_22117.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xbj_22117/04_2026/6xbj_22117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xbj_22117/04_2026/6xbj_22117.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xbj_22117/04_2026/6xbj_22117.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xbj_22117/04_2026/6xbj_22117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xbj_22117/04_2026/6xbj_22117.map"
  }
  resolution = 3.88
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    6481      2.51       5
     N    1735      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10198
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 3658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3658
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 21, 'TRANS': 443}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1736
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "S"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1785
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.51, per 1000 atoms: 0.25
  Number of scatterers: 10198
  At special positions: 0
  Unit cell: (109.956, 124.117, 163.268, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    1906      8.00
     N    1735      7.00
     C    6481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  64 " - pdb=" SG  CYS R 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  70 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  78 " - pdb=" SG  CYS R 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 118 " - pdb=" SG  CYS R 154 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 147 " - pdb=" SG  CYS R 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 193 " - pdb=" SG  CYS R 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 217 " - pdb=" SG  CYS R 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 314 " - pdb=" SG  CYS R 390 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 490 " - pdb=" SG  CYS R 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.06
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.02

  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: 0.69
  Conformation dependent library (CDL) restraints added in 505.9 milliseconds
  

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 16 sheets defined
      36.0% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 98 through 110
    Processing helix  chain 'R' and resid 111 through 114
      removed outlier: 4.293A  pdb=" N   ASN R 114 " --> pdb=" O   GLY R 111 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 111 through 114'
    Processing helix  chain 'R' and resid 115 through 130
      removed outlier: 4.384A  pdb=" N   VAL R 121 " --> pdb=" O   ARG R 117 " (cutoff:3.500A)
      Proline residue:  R 124  - end of helix
    Processing helix  chain 'R' and resid 143 through 150
      removed outlier: 3.975A  pdb=" N   CYS R 147 " --> pdb=" O   SER R 143 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR R 150 " --> pdb=" O   LEU R 146 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 161
      removed outlier: 4.162A  pdb=" N   ARG R 159 " --> pdb=" O   ALA R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 185
      removed outlier: 3.659A  pdb=" N   ASN R 184 " --> pdb=" O   GLU R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 206
      removed outlier: 3.926A  pdb=" N   TRP R 206 " --> pdb=" O   PRO R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 255
      removed outlier: 3.936A  pdb=" N   ASP R 255 " --> pdb=" O   THR R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 282
    Processing helix  chain 'R' and resid 289 through 294
    Processing helix  chain 'R' and resid 314 through 345
      removed outlier: 3.730A  pdb=" N   ALA R 345 " --> pdb=" O   THR R 341 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 351 through 355
      removed outlier: 3.895A  pdb=" N   GLY R 355 " --> pdb=" O   PRO R 352 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 356 through 378
      Proline residue:  R 368  - end of helix
    Processing helix  chain 'R' and resid 396 through 429
      removed outlier: 4.135A  pdb=" N   ARG R 400 " --> pdb=" O   ASN R 396 " (cutoff:3.500A)
      Proline residue:  R 407  - end of helix
    Processing helix  chain 'R' and resid 438 through 494
      removed outlier: 3.568A  pdb=" N   LYS R 444 " --> pdb=" O   LYS R 440 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE R 455 " --> pdb=" O   ARG R 451 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE R 460 " --> pdb=" O   GLY R 456 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL R 463 " --> pdb=" O   ALA R 459 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   THR R 466 " --> pdb=" O   PHE R 462 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASP R 473 " --> pdb=" O   CYS R 469 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASN R 476 " --> pdb=" O   TYR R 472 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   ALA R 478 " --> pdb=" O   PHE R 474 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLU R 479 " --> pdb=" O   PHE R 475 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL R 494 " --> pdb=" O   CYS R 490 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 514 through 532
      removed outlier: 4.147A  pdb=" N   GLU R 518 " --> pdb=" O   SER R 514 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   MET R 532 " --> pdb=" O   THR R 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.662A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.961A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.003A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.626A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.028A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 3.762A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 7 through 24
    Processing helix  chain 'B' and resid 29 through 36
      removed outlier: 4.178A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.877A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 52 through 56
      removed outlier: 3.908A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66
    Processing sheet with id=AA2, first strand: chain 'R' and resid 197 through 199
    Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 190
      removed outlier: 3.529A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.889A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS A 322 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 52
      removed outlier: 3.854A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.117A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 111 through 113
      removed outlier: 3.846A  pdb=" N   CYS B 121 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.575A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 191
      removed outlier: 5.349A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.687A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.451A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.445A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.843A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.576A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.576A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.454A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147
      removed outlier: 3.642A  pdb=" N   ILE S 145 " --> pdb=" O   LEU S 202 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   THR S 201 " --> pdb=" O   SER S 194 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 182 through 183
      removed outlier: 6.914A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1221 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: 1.63

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1984
        1.33 -     1.46: 2601
        1.46 -     1.58: 5737
        1.58 -     1.70: 0
        1.70 -     1.82: 105
  Bond restraints: 10427
  Sorted by residual:
  bond pdb=" N   VAL S  64 "
       pdb=" CA  VAL S  64 "
    ideal  model  delta    sigma   weight residual
    1.455  1.498 -0.042 1.04e-02 9.25e+03 1.66e+01
  bond pdb=" N   VAL B  90 "
       pdb=" CA  VAL B  90 "
    ideal  model  delta    sigma   weight residual
    1.452  1.497 -0.045 1.18e-02 7.18e+03 1.46e+01
  bond pdb=" N   VAL R 404 "
       pdb=" CA  VAL R 404 "
    ideal  model  delta    sigma   weight residual
    1.452  1.497 -0.044 1.18e-02 7.18e+03 1.42e+01
  bond pdb=" N   LEU R 367 "
       pdb=" CA  LEU R 367 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 9.20e-03 1.18e+04 1.39e+01
  bond pdb=" N   GLY B 185 "
       pdb=" CA  GLY B 185 "
    ideal  model  delta    sigma   weight residual
    1.445  1.478 -0.034 9.20e-03 1.18e+04 1.33e+01
  ... (remaining 10422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 9825
        1.85 -     3.70: 3796
        3.70 -     5.56: 491
        5.56 -     7.41: 20
        7.41 -     9.26: 2
  Bond angle restraints: 14134
  Sorted by residual:
  angle pdb=" C   TYR S 223 "
        pdb=" CA  TYR S 223 "
        pdb=" CB  TYR S 223 "
      ideal   model   delta    sigma   weight residual
     110.34  101.08    9.26 1.30e+00 5.92e-01 5.07e+01
  angle pdb=" C   GLN R 216 "
        pdb=" N   CYS R 217 "
        pdb=" CA  CYS R 217 "
      ideal   model   delta    sigma   weight residual
     120.28  127.65   -7.37 1.34e+00 5.57e-01 3.03e+01
  angle pdb=" C   GLU R 194 "
        pdb=" N   VAL R 195 "
        pdb=" CA  VAL R 195 "
      ideal   model   delta    sigma   weight residual
     120.43  125.32   -4.89 9.60e-01 1.09e+00 2.60e+01
  angle pdb=" C   GLY R 415 "
        pdb=" N   GLY R 416 "
        pdb=" CA  GLY R 416 "
      ideal   model   delta    sigma   weight residual
     119.99  125.40   -5.41 1.13e+00 7.83e-01 2.29e+01
  angle pdb=" C   PHE A 259 "
        pdb=" N   THR A 260 "
        pdb=" CA  THR A 260 "
      ideal   model   delta    sigma   weight residual
     120.38  126.90   -6.52 1.37e+00 5.33e-01 2.26e+01
  ... (remaining 14129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.29: 5928
       25.29 -    50.58: 278
       50.58 -    75.87: 19
       75.87 -   101.16: 0
      101.16 -   126.45: 1
  Dihedral angle restraints: 6226
    sinusoidal: 2479
      harmonic: 3747
  Sorted by residual:
  dihedral pdb=" CA  TYR S 223 "
           pdb=" C   TYR S 223 "
           pdb=" N   PRO S 224 "
           pdb=" CA  PRO S 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   53.55  126.45     0      5.00e+00 4.00e-02 6.40e+02
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.74  -66.74     1      1.00e+01 1.00e-02 5.81e+01
  dihedral pdb=" CB  CYS R 217 "
           pdb=" SG  CYS R 217 "
           pdb=" SG  CYS R 295 "
           pdb=" CB  CYS R 295 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.69   51.69     1      1.00e+01 1.00e-02 3.65e+01
  ... (remaining 6223 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 720
       0.057 -    0.115: 587
       0.115 -    0.172: 244
       0.172 -    0.229: 20
       0.229 -    0.286: 1
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" C13 CLR R 701 "
            pdb=" C12 CLR R 701 "
            pdb=" C14 CLR R 701 "
            pdb=" C17 CLR R 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C14 CLR R 701 "
            pdb=" C13 CLR R 701 "
            pdb=" C15 CLR R 701 "
            pdb=" C8  CLR R 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.55    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  TYR R 262 "
            pdb=" N   TYR R 262 "
            pdb=" C   TYR R 262 "
            pdb=" CB  TYR R 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1569 not shown)

  Planarity restraints: 1801
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "    0.052 5.00e-02 4.00e+02   7.89e-02 9.95e+00
        pdb=" N   PRO S 224 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 121 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.89e+00
        pdb=" C   CYS B 121 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   CYS B 121 "    0.018 2.00e-02 2.50e+03
        pdb=" N   SER B 122 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 259 "    0.010 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   PHE A 259 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   PHE A 259 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR A 260 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1798 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 320
        2.71 -     3.26: 10019
        3.26 -     3.81: 15273
        3.81 -     4.35: 19567
        4.35 -     4.90: 33005
  Nonbonded interactions: 78184
  Sorted by model distance:
  nonbonded pdb=" O   MET R 525 "
            pdb=" OG1 THR R 528 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   ILE R 375 "
            pdb=" O   VAL R 378 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.342 3.040
  ... (remaining 78179 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.590
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6248
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      :  0.014   0.060  10439  Z= 1.063
  Angle     :  1.762   9.259  14158  Z= 1.292
  Chirality :  0.082   0.286   1572
  Planarity :  0.004   0.079   1801
  Dihedral  : 13.702 126.448   3782
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.99 %
    Favored  : 93.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.08 %

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: -4.02 (0.19), residues: 1283
  helix: -1.62 (0.22), residues: 411
  sheet: -3.57 (0.28), residues: 216
  loop : -3.08 (0.20), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG S 179 
 TYR   0.024   0.003   TYR S 103 
 PHE   0.019   0.003   PHE A 334 
 TRP   0.026   0.002   TRP R 163 
 HIS   0.008   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.01385 (10427)
  covalent geometry    : angle       1.76164 (14134)
  SS BOND              : bond        0.00872 (   12)
  SS BOND              : angle       1.79534 (   24)
  hydrogen bonds       : bond        0.23048 (  428)
  hydrogen bonds       : angle       8.27082 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 287
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   74 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6766 (tpt90)
REVERT: R  237 PHE cc_start: 0.7163 (t80) cc_final: 0.6641 (t80)
REVERT: R  261 ARG cc_start: 0.5099 (ptt-90) cc_final: 0.4857 (ptt-90)
REVERT: R  301 MET cc_start: 0.8609 (ptp) cc_final: 0.8054 (ptp)
REVERT: R  339 TRP cc_start: 0.7367 (m-10) cc_final: 0.6973 (m-10)
REVERT: R  381 VAL cc_start: 0.6174 (OUTLIER) cc_final: 0.5743 (p)
REVERT: R  397 TYR cc_start: 0.7588 (p90) cc_final: 0.7375 (p90)
REVERT: R  424 MET cc_start: 0.8881 (mtm) cc_final: 0.8570 (mtm)
REVERT: R  439 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7703 (tp30)
REVERT: R  473 ASP cc_start: 0.8618 (t0) cc_final: 0.8351 (t0)
REVERT: R  475 PHE cc_start: 0.5459 (m-80) cc_final: 0.4983 (m-10)
REVERT: R  480 TRP cc_start: 0.7432 (m-10) cc_final: 0.7113 (m-90)
REVERT: R  482 ARG cc_start: 0.7839 (tmm-80) cc_final: 0.7398 (mpt180)
REVERT: R  486 ASP cc_start: 0.8086 (m-30) cc_final: 0.7376 (m-30)
REVERT: R  526 PHE cc_start: 0.7629 (m-10) cc_final: 0.7420 (m-80)
REVERT: R  532 MET cc_start: 0.7814 (mmt) cc_final: 0.7546 (mmt)
REVERT: A    8 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7953 (mt-10)
REVERT: A  200 ASP cc_start: 0.7996 (p0) cc_final: 0.7552 (t0)
REVERT: A  242 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.6900 (mmt180)
REVERT: A  243 MET cc_start: 0.7368 (tpp) cc_final: 0.7048 (tpp)
REVERT: A  275 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8335 (tt0)
REVERT: A  277 LYS cc_start: 0.8117 (tptt) cc_final: 0.7812 (tppt)
REVERT: A  302 TYR cc_start: 0.7625 (t80) cc_final: 0.7194 (t80)
REVERT: B   20 ASP cc_start: 0.8974 (t0) cc_final: 0.8771 (t0)
REVERT: B   36 ASN cc_start: 0.8418 (t0) cc_final: 0.8186 (t0)
REVERT: B   37 ILE cc_start: 0.8993 (tp) cc_final: 0.8644 (tp)
REVERT: B   95 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7484 (pp)
REVERT: B  138 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7381 (pp20)
REVERT: B  188 MET cc_start: 0.8194 (mmm) cc_final: 0.7953 (mmm)
REVERT: B  189 SER cc_start: 0.8613 (t) cc_final: 0.8298 (t)
REVERT: B  215 GLU cc_start: 0.8196 (mp0) cc_final: 0.7445 (mp0)
REVERT: B  217 MET cc_start: 0.7107 (ptp) cc_final: 0.6887 (ptp)
REVERT: B  228 ASP cc_start: 0.7689 (m-30) cc_final: 0.6515 (m-30)
REVERT: B  260 GLU cc_start: 0.8671 (tt0) cc_final: 0.8138 (tt0)
REVERT: B  284 LEU cc_start: 0.7605 (pt) cc_final: 0.7235 (pt)
REVERT: B  295 ASN cc_start: 0.8514 (m-40) cc_final: 0.8136 (m-40)
REVERT: B  297 TRP cc_start: 0.8319 (m100) cc_final: 0.7691 (m100)
REVERT: B  325 MET cc_start: 0.8160 (mmm) cc_final: 0.7791 (tpt)
REVERT: B  339 TRP cc_start: 0.8243 (m100) cc_final: 0.7772 (m100)
REVERT: G   18 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6006 (tm-30)
REVERT: G   21 MET cc_start: 0.7900 (ttp) cc_final: 0.7507 (tmm)
REVERT: G   38 MET cc_start: 0.7914 (tmm) cc_final: 0.7574 (tpp)
REVERT: G   42 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8038 (pp20)
REVERT: G   48 ASP cc_start: 0.6960 (t70) cc_final: 0.6748 (t0)
REVERT: S    3 GLN cc_start: 0.7014 (tp40) cc_final: 0.6485 (tt0)
REVERT: S   87 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6915 (mtt90)
REVERT: S   89 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8714 (mm-30)
REVERT: S  125 ASP cc_start: 0.8072 (p0) cc_final: 0.7789 (p0)
REVERT: S  141 GLU cc_start: 0.7343 (mp0) cc_final: 0.6794 (mp0)
REVERT: S  180 MET cc_start: 0.8478 (ptm) cc_final: 0.7595 (ptm)
REVERT: S  208 GLU cc_start: 0.8370 (pt0) cc_final: 0.7778 (pm20)
REVERT: S  211 ASP cc_start: 0.8641 (t0) cc_final: 0.8156 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1211
  time to fit residues: 47.2170
Evaluate side-chains
  208 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  381 VAL
Chi-restraints excluded: chain B residue   95 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    0.6980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0970
   chunk 122 optimal weight:    0.0980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
R  99 GLN
R 114 ASN
R 136 ASN
R 180 ASN
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 433 HIS
R 511 ASN
B  91 HIS
B 340 ASN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.142722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.098752 restraints weight = 16386.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.101578 restraints weight = 8865.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.103448 restraints weight = 5985.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.104542 restraints weight = 4670.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.105416 restraints weight = 4020.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10439  Z= 0.133
  Angle     :  0.645  11.529  14158  Z= 0.329
  Chirality :  0.041   0.216   1572
  Planarity :  0.004   0.068   1801
  Dihedral  :  6.272  69.152   1478
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.52 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.22), residues: 1283
  helix:  0.51 (0.25), residues: 423
  sheet: -3.03 (0.27), residues: 255
  loop : -2.37 (0.22), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.016   0.002   TYR R 472 
 PHE   0.013   0.001   PHE R 318 
 TRP   0.014   0.001   TRP R 163 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10427)
  covalent geometry    : angle       0.64279 (14134)
  SS BOND              : bond        0.00516 (   12)
  SS BOND              : angle       1.54538 (   24)
  hydrogen bonds       : bond        0.04332 (  428)
  hydrogen bonds       : angle       5.14274 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 244
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  237 PHE cc_start: 0.8438 (t80) cc_final: 0.8148 (t80)
REVERT: R  305 GLU cc_start: 0.6416 (tp30) cc_final: 0.6068 (tp30)
REVERT: R  339 TRP cc_start: 0.9006 (m-10) cc_final: 0.8200 (m-90)
REVERT: R  397 TYR cc_start: 0.8075 (p90) cc_final: 0.7724 (p90)
REVERT: R  475 PHE cc_start: 0.6360 (m-80) cc_final: 0.5709 (m-10)
REVERT: R  481 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7588 (tp30)
REVERT: R  485 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8308 (ptm-80)
REVERT: A  200 ASP cc_start: 0.7749 (p0) cc_final: 0.7410 (t0)
REVERT: A  230 TYR cc_start: 0.8526 (p90) cc_final: 0.8244 (p90)
REVERT: A  313 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (ptp90)
REVERT: B   15 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8951 (mtpt)
REVERT: B   61 MET cc_start: 0.8037 (ptm) cc_final: 0.7717 (ttm)
REVERT: B   82 TRP cc_start: 0.9190 (m100) cc_final: 0.8438 (m100)
REVERT: B   95 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8642 (pp)
REVERT: B  188 MET cc_start: 0.9048 (mmm) cc_final: 0.8733 (mmm)
REVERT: B  228 ASP cc_start: 0.8338 (m-30) cc_final: 0.7866 (m-30)
REVERT: G   18 GLN cc_start: 0.7518 (tm-30) cc_final: 0.6869 (tm-30)
REVERT: S    3 GLN cc_start: 0.8163 (tp40) cc_final: 0.7738 (tt0)
REVERT: S  141 GLU cc_start: 0.8172 (mp0) cc_final: 0.7718 (mp0)
REVERT: S  180 MET cc_start: 0.8635 (ptm) cc_final: 0.7915 (ptm)
  outliers start: 32
  outliers final: 11
  residues processed: 266
  average time/residue: 0.1085
  time to fit residues: 39.5558
Evaluate side-chains
  207 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 193
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  470 HIS
Chi-restraints excluded: chain R residue  485 ARG
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  129 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:   20.0000
   chunk 96 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 118 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 110 optimal weight:    0.0670
   overall best weight:    2.3724

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

Flipped N/Q/H residues before XYZ refinement:
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 511 ASN
A 256 ASN
B 237 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.138298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.101859 restraints weight = 16779.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.101199 restraints weight = 11193.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.101695 restraints weight = 10895.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.104134 restraints weight = 7538.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.104400 restraints weight = 5466.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10439  Z= 0.214
  Angle     :  0.672  11.957  14158  Z= 0.341
  Chirality :  0.043   0.176   1572
  Planarity :  0.004   0.067   1801
  Dihedral  :  6.116  59.082   1477
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.79 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.93 (0.23), residues: 1283
  helix:  0.92 (0.25), residues: 425
  sheet: -2.75 (0.29), residues: 248
  loop : -2.26 (0.23), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 261 
 TYR   0.016   0.002   TYR B 264 
 PHE   0.015   0.001   PHE R 318 
 TRP   0.020   0.002   TRP B 297 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 (10427)
  covalent geometry    : angle       0.66982 (14134)
  SS BOND              : bond        0.00498 (   12)
  SS BOND              : angle       1.47154 (   24)
  hydrogen bonds       : bond        0.04329 (  428)
  hydrogen bonds       : angle       5.00167 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 202
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  158 GLU cc_start: 0.7465 (pt0) cc_final: 0.7198 (pm20)
REVERT: R  237 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8229 (t80)
REVERT: R  257 ARG cc_start: 0.7020 (mmm160) cc_final: 0.6774 (ptp-170)
REVERT: R  339 TRP cc_start: 0.9117 (m-10) cc_final: 0.8338 (m-90)
REVERT: R  454 ILE cc_start: 0.8392 (mt) cc_final: 0.8110 (mt)
REVERT: R  475 PHE cc_start: 0.6352 (m-80) cc_final: 0.5613 (m-10)
REVERT: A  242 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7856 (mmt180)
REVERT: B   15 LYS cc_start: 0.9206 (ttmt) cc_final: 0.8949 (mtpt)
REVERT: B   59 TYR cc_start: 0.9327 (m-80) cc_final: 0.9079 (m-80)
REVERT: B   82 TRP cc_start: 0.9302 (m100) cc_final: 0.8513 (m100)
REVERT: B   95 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8834 (pp)
REVERT: B  138 GLU cc_start: 0.7218 (pp20) cc_final: 0.6860 (pp20)
REVERT: B  188 MET cc_start: 0.9016 (mmm) cc_final: 0.8656 (mmm)
REVERT: B  228 ASP cc_start: 0.8376 (m-30) cc_final: 0.7921 (m-30)
REVERT: B  339 TRP cc_start: 0.8964 (m100) cc_final: 0.8641 (m100)
REVERT: G   48 ASP cc_start: 0.8924 (t0) cc_final: 0.8698 (t0)
REVERT: S  141 GLU cc_start: 0.8218 (mp0) cc_final: 0.7732 (mp0)
REVERT: S  160 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8672 (p)
REVERT: S  180 MET cc_start: 0.8750 (ptm) cc_final: 0.8115 (ptm)
  outliers start: 44
  outliers final: 23
  residues processed: 232
  average time/residue: 0.1031
  time to fit residues: 33.4691
Evaluate side-chains
  212 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 186
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  131 MET
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  307 THR
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  470 HIS
Chi-restraints excluded: chain R residue  530 ILE
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 127 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 511 ASN
G  18 GLN
G  59 ASN
S 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.141169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.096850 restraints weight = 16729.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.099696 restraints weight = 9028.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.101615 restraints weight = 6093.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.102742 restraints weight = 4738.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.103586 restraints weight = 4069.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10439  Z= 0.134
  Angle     :  0.636  11.298  14158  Z= 0.317
  Chirality :  0.041   0.156   1572
  Planarity :  0.004   0.062   1801
  Dihedral  :  5.882  56.097   1477
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 16.24 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.61 (0.23), residues: 1283
  helix:  1.12 (0.25), residues: 431
  sheet: -2.52 (0.30), residues: 246
  loop : -2.07 (0.23), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG R 117 
 TYR   0.019   0.001   TYR A 302 
 PHE   0.011   0.001   PHE R 318 
 TRP   0.027   0.002   TRP R 119 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10427)
  covalent geometry    : angle       0.63547 (14134)
  SS BOND              : bond        0.00318 (   12)
  SS BOND              : angle       1.03070 (   24)
  hydrogen bonds       : bond        0.03838 (  428)
  hydrogen bonds       : angle       4.72141 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 210
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  237 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8129 (t80)
REVERT: R  246 LEU cc_start: 0.8988 (tp) cc_final: 0.8731 (mt)
REVERT: R  257 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6787 (ptp-170)
REVERT: R  261 ARG cc_start: 0.6834 (ptt-90) cc_final: 0.6511 (mtm-85)
REVERT: R  339 TRP cc_start: 0.8965 (m-10) cc_final: 0.8137 (m-90)
REVERT: R  397 TYR cc_start: 0.8014 (p90) cc_final: 0.7683 (p90)
REVERT: R  454 ILE cc_start: 0.8253 (mt) cc_final: 0.7940 (mt)
REVERT: R  475 PHE cc_start: 0.6265 (m-80) cc_final: 0.5498 (m-10)
REVERT: A  277 LYS cc_start: 0.8918 (tptt) cc_final: 0.8652 (tppt)
REVERT: B   15 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8995 (mtpt)
REVERT: B   95 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8746 (pp)
REVERT: B  138 GLU cc_start: 0.7400 (pp20) cc_final: 0.6885 (pp20)
REVERT: B  188 MET cc_start: 0.9051 (mmm) cc_final: 0.8706 (mmm)
REVERT: B  338 ILE cc_start: 0.9160 (mt) cc_final: 0.8921 (mm)
REVERT: B  339 TRP cc_start: 0.8893 (m100) cc_final: 0.8682 (m100)
REVERT: G   19 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8938 (mm)
REVERT: G   21 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6834 (tmm)
REVERT: S  128 MET cc_start: 0.8391 (mmm) cc_final: 0.7812 (mmm)
REVERT: S  141 GLU cc_start: 0.8122 (mp0) cc_final: 0.7773 (mp0)
REVERT: S  180 MET cc_start: 0.8676 (ptm) cc_final: 0.7945 (ptm)
REVERT: S  223 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8336 (t80)
  outliers start: 48
  outliers final: 27
  residues processed: 241
  average time/residue: 0.0994
  time to fit residues: 33.8230
Evaluate side-chains
  223 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 191
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  117 ARG
Chi-restraints excluded: chain R residue  131 MET
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  530 ILE
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 106 optimal weight:    0.6980
   chunk 95 optimal weight:    0.4980
   chunk 119 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 511 ASN
A 256 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.137718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.101021 restraints weight = 16713.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.100627 restraints weight = 10606.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.101183 restraints weight = 10469.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.103528 restraints weight = 7191.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103733 restraints weight = 5247.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10439  Z= 0.232
  Angle     :  0.683  12.264  14158  Z= 0.348
  Chirality :  0.043   0.192   1572
  Planarity :  0.004   0.062   1801
  Dihedral  :  5.956  54.836   1477
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 16.33 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.64 (0.23), residues: 1283
  helix:  1.01 (0.25), residues: 444
  sheet: -2.47 (0.30), residues: 252
  loop : -2.12 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 117 
 TYR   0.019   0.002   TYR A 302 
 PHE   0.017   0.002   PHE B 241 
 TRP   0.033   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 (10427)
  covalent geometry    : angle       0.67833 (14134)
  SS BOND              : bond        0.00382 (   12)
  SS BOND              : angle       2.12014 (   24)
  hydrogen bonds       : bond        0.04138 (  428)
  hydrogen bonds       : angle       4.80233 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 192
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: R  237 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8204 (t80)
REVERT: R  246 LEU cc_start: 0.9000 (tp) cc_final: 0.8770 (mt)
REVERT: R  257 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6833 (ptp-170)
REVERT: R  339 TRP cc_start: 0.9091 (m-10) cc_final: 0.8288 (m-90)
REVERT: R  397 TYR cc_start: 0.8065 (p90) cc_final: 0.7628 (p90)
REVERT: R  454 ILE cc_start: 0.8395 (mt) cc_final: 0.8182 (mt)
REVERT: A  277 LYS cc_start: 0.8939 (tptt) cc_final: 0.8642 (tppt)
REVERT: B   15 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8994 (mtpt)
REVERT: B   47 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9092 (p)
REVERT: B   59 TYR cc_start: 0.9328 (m-80) cc_final: 0.8931 (m-80)
REVERT: B  138 GLU cc_start: 0.7651 (pp20) cc_final: 0.7216 (pp20)
REVERT: B  188 MET cc_start: 0.9004 (mmm) cc_final: 0.8675 (mmm)
REVERT: B  339 TRP cc_start: 0.8963 (m100) cc_final: 0.8414 (m100)
REVERT: G   21 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6893 (tmm)
REVERT: S   82 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6311 (mm-40)
REVERT: S  128 MET cc_start: 0.8340 (mmm) cc_final: 0.7739 (mmm)
REVERT: S  141 GLU cc_start: 0.8215 (mp0) cc_final: 0.7845 (mp0)
REVERT: S  160 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8673 (p)
REVERT: S  180 MET cc_start: 0.8787 (ptm) cc_final: 0.8062 (ptm)
  outliers start: 63
  outliers final: 44
  residues processed: 234
  average time/residue: 0.0973
  time to fit residues: 32.3987
Evaluate side-chains
  230 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 182
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  117 ARG
Chi-restraints excluded: chain R residue  131 MET
Chi-restraints excluded: chain R residue  145 THR
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  279 ILE
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  317 ILE
Chi-restraints excluded: chain R residue  341 THR
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  382 ASP
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  470 HIS
Chi-restraints excluded: chain R residue  507 CYS
Chi-restraints excluded: chain R residue  516 LEU
Chi-restraints excluded: chain R residue  530 ILE
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  142 SER
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 120 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 90 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0060
   chunk 69 optimal weight:    0.0870
   chunk 44 optimal weight:    0.6980
   chunk 23 optimal weight:   20.0000
   chunk 121 optimal weight:    0.7980
   overall best weight:    0.3574

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

Flipped N/Q/H residues before XYZ refinement:
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
A 256 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.144718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.107451 restraints weight = 16769.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107697 restraints weight = 10476.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108304 restraints weight = 9970.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.110693 restraints weight = 6745.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110854 restraints weight = 4839.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10439  Z= 0.118
  Angle     :  0.655  14.296  14158  Z= 0.323
  Chirality :  0.042   0.247   1572
  Planarity :  0.004   0.062   1801
  Dihedral  :  5.637  51.006   1477
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.06 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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 (0.23), residues: 1283
  helix:  1.25 (0.25), residues: 435
  sheet: -2.24 (0.30), residues: 249
  loop : -1.93 (0.24), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 113 
 TYR   0.021   0.001   TYR S  50 
 PHE   0.009   0.001   PHE S 227 
 TRP   0.024   0.002   TRP B 297 
 HIS   0.008   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10427)
  covalent geometry    : angle       0.65405 (14134)
  SS BOND              : bond        0.00212 (   12)
  SS BOND              : angle       0.90901 (   24)
  hydrogen bonds       : bond        0.03616 (  428)
  hydrogen bonds       : angle       4.52023 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 210
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  246 LEU cc_start: 0.8899 (tp) cc_final: 0.8697 (mt)
REVERT: R  257 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6775 (ptp-170)
REVERT: R  261 ARG cc_start: 0.6845 (ptt-90) cc_final: 0.6587 (mtm-85)
REVERT: R  339 TRP cc_start: 0.8956 (m-10) cc_final: 0.8173 (m-90)
REVERT: R  397 TYR cc_start: 0.7968 (p90) cc_final: 0.7680 (p90)
REVERT: R  454 ILE cc_start: 0.8399 (mt) cc_final: 0.8052 (mt)
REVERT: R  475 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5956 (m-80)
REVERT: B   15 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8987 (mtpt)
REVERT: B   59 TYR cc_start: 0.9086 (m-80) cc_final: 0.8879 (m-80)
REVERT: B   82 TRP cc_start: 0.9246 (m100) cc_final: 0.8532 (m100)
REVERT: B  138 GLU cc_start: 0.7628 (pp20) cc_final: 0.7132 (pp20)
REVERT: B  188 MET cc_start: 0.8997 (mmm) cc_final: 0.8677 (mmm)
REVERT: B  338 ILE cc_start: 0.9132 (mt) cc_final: 0.8879 (mm)
REVERT: B  339 TRP cc_start: 0.8903 (m100) cc_final: 0.8389 (m100)
REVERT: G   21 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6790 (tmm)
REVERT: S  128 MET cc_start: 0.8180 (mmm) cc_final: 0.7575 (mmm)
REVERT: S  141 GLU cc_start: 0.8166 (mp0) cc_final: 0.7806 (mp0)
REVERT: S  180 MET cc_start: 0.8601 (ptm) cc_final: 0.7896 (ptm)
REVERT: S  222 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7594 (mm-30)
  outliers start: 46
  outliers final: 30
  residues processed: 240
  average time/residue: 0.0962
  time to fit residues: 32.8349
Evaluate side-chains
  223 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 191
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  145 THR
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  382 ASP
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  507 CYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 90 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
B   9 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.143363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.106413 restraints weight = 16722.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.105246 restraints weight = 11171.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.105922 restraints weight = 10908.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.108442 restraints weight = 7472.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108725 restraints weight = 5350.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10439  Z= 0.144
  Angle     :  0.660  13.222  14158  Z= 0.328
  Chirality :  0.042   0.196   1572
  Planarity :  0.004   0.063   1801
  Dihedral  :  5.655  48.940   1477
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.87 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.32 (0.23), residues: 1283
  helix:  1.27 (0.25), residues: 436
  sheet: -2.20 (0.31), residues: 245
  loop : -1.94 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 485 
 TYR   0.009   0.001   TYR R  75 
 PHE   0.019   0.001   PHE R 237 
 TRP   0.042   0.002   TRP B 297 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10427)
  covalent geometry    : angle       0.65873 (14134)
  SS BOND              : bond        0.00362 (   12)
  SS BOND              : angle       1.28809 (   24)
  hydrogen bonds       : bond        0.03710 (  428)
  hydrogen bonds       : angle       4.54594 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 201
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: R  261 ARG cc_start: 0.6797 (ptt-90) cc_final: 0.6535 (mtm-85)
REVERT: R  339 TRP cc_start: 0.9011 (m-10) cc_final: 0.8194 (m-90)
REVERT: R  397 TYR cc_start: 0.8011 (p90) cc_final: 0.7665 (p90)
REVERT: R  454 ILE cc_start: 0.8400 (mt) cc_final: 0.8075 (mt)
REVERT: R  475 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5932 (m-80)
REVERT: A  277 LYS cc_start: 0.8925 (tptt) cc_final: 0.8702 (tppt)
REVERT: A  294 ASN cc_start: 0.7676 (m110) cc_final: 0.6915 (t0)
REVERT: B   15 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8987 (mtpt)
REVERT: B   59 TYR cc_start: 0.9180 (m-80) cc_final: 0.8953 (m-80)
REVERT: B   82 TRP cc_start: 0.9268 (m100) cc_final: 0.8549 (m100)
REVERT: B  138 GLU cc_start: 0.7787 (pp20) cc_final: 0.7291 (pp20)
REVERT: B  188 MET cc_start: 0.8984 (mmm) cc_final: 0.8632 (mmm)
REVERT: B  339 TRP cc_start: 0.8793 (m100) cc_final: 0.8425 (m100)
REVERT: G   21 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6813 (tmm)
REVERT: S   82 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6312 (mm-40)
REVERT: S  128 MET cc_start: 0.8205 (mmm) cc_final: 0.7599 (mmm)
REVERT: S  141 GLU cc_start: 0.8149 (mp0) cc_final: 0.7754 (mp0)
REVERT: S  160 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8860 (p)
REVERT: S  180 MET cc_start: 0.8672 (ptm) cc_final: 0.7930 (ptm)
REVERT: S  222 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7594 (mm-30)
  outliers start: 43
  outliers final: 34
  residues processed: 232
  average time/residue: 0.0979
  time to fit residues: 32.4517
Evaluate side-chains
  221 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  117 ARG
Chi-restraints excluded: chain R residue  145 THR
Chi-restraints excluded: chain R residue  234 ILE
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  382 ASP
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  507 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  100 ILE
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 59 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 106 optimal weight:    0.1980
   chunk 54 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0060
   chunk 109 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0050
   chunk 93 optimal weight:    0.2980
   overall best weight:    0.3012

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

Flipped N/Q/H residues before XYZ refinement:
R 218 GLN
R 511 ASN
A 204 GLN
B   9 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.147510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.110159 restraints weight = 16596.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110134 restraints weight = 11074.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.110765 restraints weight = 10237.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.113205 restraints weight = 7114.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.113271 restraints weight = 5192.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10439  Z= 0.113
  Angle     :  0.647  13.561  14158  Z= 0.319
  Chirality :  0.041   0.217   1572
  Planarity :  0.004   0.061   1801
  Dihedral  :  5.391  46.052   1477
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.69 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.16 (0.23), residues: 1283
  helix:  1.36 (0.25), residues: 443
  sheet: -2.02 (0.31), residues: 243
  loop : -1.90 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S  18 
 TYR   0.020   0.001   TYR R 472 
 PHE   0.010   0.001   PHE R 237 
 TRP   0.021   0.001   TRP B 211 
 HIS   0.008   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10427)
  covalent geometry    : angle       0.64618 (14134)
  SS BOND              : bond        0.00424 (   12)
  SS BOND              : angle       1.10452 (   24)
  hydrogen bonds       : bond        0.03496 (  428)
  hydrogen bonds       : angle       4.49666 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  339 TRP cc_start: 0.8916 (m-10) cc_final: 0.8148 (m-90)
REVERT: R  366 SER cc_start: 0.8541 (m) cc_final: 0.8273 (m)
REVERT: R  454 ILE cc_start: 0.8358 (mt) cc_final: 0.8014 (mt)
REVERT: R  475 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.5660 (m-80)
REVERT: A   18 MET cc_start: 0.7599 (tmm) cc_final: 0.7302 (tmm)
REVERT: A  277 LYS cc_start: 0.8911 (tptt) cc_final: 0.8676 (tppt)
REVERT: A  294 ASN cc_start: 0.7647 (m110) cc_final: 0.6904 (t0)
REVERT: B   15 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8963 (mtpt)
REVERT: B   82 TRP cc_start: 0.9200 (m100) cc_final: 0.8515 (m100)
REVERT: B  138 GLU cc_start: 0.7765 (pp20) cc_final: 0.7343 (pp20)
REVERT: B  188 MET cc_start: 0.9019 (mmm) cc_final: 0.8695 (mmm)
REVERT: G   21 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6738 (tmm)
REVERT: S  128 MET cc_start: 0.8120 (mmm) cc_final: 0.7531 (mmm)
REVERT: S  141 GLU cc_start: 0.8134 (mp0) cc_final: 0.7779 (mp0)
REVERT: S  160 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8882 (p)
REVERT: S  180 MET cc_start: 0.8536 (ptm) cc_final: 0.7811 (ptm)
  outliers start: 35
  outliers final: 26
  residues processed: 236
  average time/residue: 0.0985
  time to fit residues: 32.7273
Evaluate side-chains
  218 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  117 ARG
Chi-restraints excluded: chain R residue  145 THR
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  382 ASP
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  507 CYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 120 optimal weight:    0.0050
   chunk 29 optimal weight:    0.3980
   chunk 117 optimal weight:    0.1980
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
S 155 HIS

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 = 0.148385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.111479 restraints weight = 16739.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.111236 restraints weight = 11965.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.112269 restraints weight = 11352.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.112644 restraints weight = 6611.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.113675 restraints weight = 5891.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10439  Z= 0.120
  Angle     :  0.662  15.825  14158  Z= 0.327
  Chirality :  0.042   0.222   1572
  Planarity :  0.005   0.116   1801
  Dihedral  :  5.248  45.288   1477
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.60 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.09 (0.24), residues: 1283
  helix:  1.42 (0.25), residues: 443
  sheet: -1.98 (0.31), residues: 245
  loop : -1.85 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 261 
 TYR   0.017   0.001   TYR R 472 
 PHE   0.014   0.001   PHE R 237 
 TRP   0.050   0.002   TRP R 119 
 HIS   0.008   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10427)
  covalent geometry    : angle       0.66071 (14134)
  SS BOND              : bond        0.00457 (   12)
  SS BOND              : angle       1.15669 (   24)
  hydrogen bonds       : bond        0.03469 (  428)
  hydrogen bonds       : angle       4.45193 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 197
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  339 TRP cc_start: 0.8932 (m-10) cc_final: 0.8120 (m-90)
REVERT: R  366 SER cc_start: 0.8501 (m) cc_final: 0.8234 (m)
REVERT: R  454 ILE cc_start: 0.8382 (mt) cc_final: 0.8055 (mt)
REVERT: R  475 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.5206 (m-10)
REVERT: A   18 MET cc_start: 0.7586 (tmm) cc_final: 0.7288 (tmm)
REVERT: A  277 LYS cc_start: 0.8911 (tptt) cc_final: 0.8515 (tppt)
REVERT: A  294 ASN cc_start: 0.7587 (m110) cc_final: 0.6853 (t0)
REVERT: B   15 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8991 (mtpt)
REVERT: B   82 TRP cc_start: 0.9202 (m100) cc_final: 0.8526 (m100)
REVERT: B  138 GLU cc_start: 0.7841 (pp20) cc_final: 0.7616 (pp20)
REVERT: B  188 MET cc_start: 0.8990 (mmm) cc_final: 0.8664 (mmm)
REVERT: G   21 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6758 (tmm)
REVERT: S   36 TRP cc_start: 0.9291 (m100) cc_final: 0.9037 (m100)
REVERT: S   82 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6301 (mm-40)
REVERT: S  128 MET cc_start: 0.8132 (mmm) cc_final: 0.7497 (mmm)
REVERT: S  141 GLU cc_start: 0.8070 (mp0) cc_final: 0.7863 (mp0)
REVERT: S  180 MET cc_start: 0.8500 (ptm) cc_final: 0.7861 (ptm)
  outliers start: 37
  outliers final: 32
  residues processed: 224
  average time/residue: 0.0963
  time to fit residues: 30.6613
Evaluate side-chains
  217 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 183
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  117 ARG
Chi-restraints excluded: chain R residue  145 THR
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  371 LEU
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  382 ASP
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  507 CYS
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 118 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.145043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.107909 restraints weight = 16700.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107813 restraints weight = 11729.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.108758 restraints weight = 11360.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109212 restraints weight = 6893.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111655 restraints weight = 6020.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10439  Z= 0.163
  Angle     :  0.698  15.825  14158  Z= 0.346
  Chirality :  0.043   0.185   1572
  Planarity :  0.005   0.122   1801
  Dihedral  :  5.369  44.443   1477
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.14 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.15 (0.24), residues: 1283
  helix:  1.38 (0.25), residues: 443
  sheet: -2.09 (0.29), residues: 262
  loop : -1.83 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  32 
 TYR   0.015   0.001   TYR A 302 
 PHE   0.026   0.001   PHE R 237 
 TRP   0.051   0.002   TRP B 297 
 HIS   0.007   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10427)
  covalent geometry    : angle       0.69659 (14134)
  SS BOND              : bond        0.00517 (   12)
  SS BOND              : angle       1.37446 (   24)
  hydrogen bonds       : bond        0.03723 (  428)
  hydrogen bonds       : angle       4.58932 ( 1221)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: R  339 TRP cc_start: 0.8996 (m-10) cc_final: 0.8413 (m-10)
REVERT: R  366 SER cc_start: 0.8522 (m) cc_final: 0.8261 (m)
REVERT: R  454 ILE cc_start: 0.8409 (mt) cc_final: 0.8158 (mt)
REVERT: R  475 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5758 (m-80)
REVERT: A  277 LYS cc_start: 0.8847 (tptt) cc_final: 0.8622 (tppt)
REVERT: A  294 ASN cc_start: 0.7670 (m110) cc_final: 0.6911 (t0)
REVERT: B   15 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8980 (mtpt)
REVERT: B   61 MET cc_start: 0.8048 (ttm) cc_final: 0.7815 (ttm)
REVERT: B   82 TRP cc_start: 0.9261 (m100) cc_final: 0.8557 (m100)
REVERT: B  138 GLU cc_start: 0.7916 (pp20) cc_final: 0.7661 (pp20)
REVERT: B  188 MET cc_start: 0.8951 (mmm) cc_final: 0.8599 (mmm)
REVERT: G   21 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6745 (tmm)
REVERT: S  141 GLU cc_start: 0.8155 (mp0) cc_final: 0.7792 (mp0)
REVERT: S  180 MET cc_start: 0.8622 (ptm) cc_final: 0.7930 (ptm)
  outliers start: 34
  outliers final: 31
  residues processed: 214
  average time/residue: 0.0945
  time to fit residues: 29.3082
Evaluate side-chains
  214 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 181
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue  117 ARG
Chi-restraints excluded: chain R residue  145 THR
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  376 LEU
Chi-restraints excluded: chain R residue  382 ASP
Chi-restraints excluded: chain R residue  392 VAL
Chi-restraints excluded: chain R residue  424 MET
Chi-restraints excluded: chain R residue  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  507 CYS
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 106 optimal weight:    0.4980
   chunk 59 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 95 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 118 optimal weight:    0.0870
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.146570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.109538 restraints weight = 16712.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.110490 restraints weight = 12019.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.111256 restraints weight = 10441.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111657 restraints weight = 6429.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113760 restraints weight = 5658.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10439  Z= 0.134
  Angle     :  0.695  16.406  14158  Z= 0.341
  Chirality :  0.042   0.182   1572
  Planarity :  0.005   0.114   1801
  Dihedral  :  5.348  44.010   1477
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.14 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.13 (0.24), residues: 1283
  helix:  1.38 (0.25), residues: 443
  sheet: -2.12 (0.29), residues: 256
  loop : -1.78 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.018   0.001   TYR R 472 
 PHE   0.020   0.001   PHE R 237 
 TRP   0.037   0.002   TRP B 297 
 HIS   0.008   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10427)
  covalent geometry    : angle       0.69388 (14134)
  SS BOND              : bond        0.00446 (   12)
  SS BOND              : angle       1.15831 (   24)
  hydrogen bonds       : bond        0.03663 (  428)
  hydrogen bonds       : angle       4.54069 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1872.18 seconds
wall clock time: 33 minutes 7.73 seconds (1987.73 seconds total)