Starting phenix.real_space_refine
on Mon Jul 28 12:01:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xbj_22117/07_2025/6xbj_22117.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xbj_22117/07_2025/6xbj_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xbj_22117/07_2025/6xbj_22117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xbj_22117/07_2025/6xbj_22117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xbj_22117/07_2025/6xbj_22117.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xbj_22117/07_2025/6xbj_22117.cif"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.24, per 1000 atoms: 0.61
  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: 2.50
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.09
  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: 3.39

  Time building geometry restraints manager: 2.98 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:             1.260
  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:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.250
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.140
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.026   0.002   TRP R 163 
 HIS   0.008   0.002   HIS B  54 
 PHE   0.019   0.003   PHE A 334 
 TYR   0.024   0.003   TYR S 103 
 ARG   0.006   0.001   ARG S 179 

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

*********************** 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  : 1.128 
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: 0.8477 (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: 0.2578
  time to fit residues: 100.0709
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  : 1.193 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 74 optimal weight:    0.5980
   chunk 116 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 433 HIS
R 511 ASN
A 213 HIS
B  91 HIS
B 237 ASN
B 340 ASN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.141725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.097645 restraints weight = 16297.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.100419 restraints weight = 8920.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.102253 restraints weight = 6049.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10439  Z= 0.138
  Angle     :  0.649  11.681  14158  Z= 0.332
  Chirality :  0.041   0.219   1572
  Planarity :  0.004   0.071   1801
  Dihedral  :  6.294  71.794   1478
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.22), residues: 1283
  helix:  0.43 (0.25), residues: 423
  sheet: -3.04 (0.28), residues: 255
  loop : -2.41 (0.22), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 163 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.014   0.001   PHE R 318 
 TYR   0.014   0.001   TYR R 472 
 ARG   0.005   0.000   ARG A  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  428)
  hydrogen bonds       : angle       5.21883 ( 1221)
  SS BOND              : bond        0.00410 (   12)
  SS BOND              : angle       1.49390 (   24)
  covalent geometry    : bond        0.00312 (10427)
  covalent geometry    : angle       0.64636 (14134)

*********************** 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
  272 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 241
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  159 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7216 (ttp-170)
REVERT: R  237 PHE cc_start: 0.8462 (t80) cc_final: 0.8184 (t80)
REVERT: R  305 GLU cc_start: 0.6348 (tp30) cc_final: 0.6004 (tp30)
REVERT: R  339 TRP cc_start: 0.9041 (m-10) cc_final: 0.8209 (m-90)
REVERT: R  397 TYR cc_start: 0.8117 (p90) cc_final: 0.7764 (p90)
REVERT: R  475 PHE cc_start: 0.6388 (m-80) cc_final: 0.5682 (m-10)
REVERT: R  481 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7606 (tp30)
REVERT: A  200 ASP cc_start: 0.7762 (p0) cc_final: 0.7438 (t0)
REVERT: A  230 TYR cc_start: 0.8589 (p90) cc_final: 0.8360 (p90)
REVERT: A  302 TYR cc_start: 0.8666 (t80) cc_final: 0.8163 (t80)
REVERT: A  313 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8468 (ptp90)
REVERT: B   15 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8954 (mtpt)
REVERT: B   61 MET cc_start: 0.8083 (ptm) cc_final: 0.7702 (ttm)
REVERT: B   82 TRP cc_start: 0.9226 (m100) cc_final: 0.8480 (m100)
REVERT: B   95 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8687 (pp)
REVERT: B  188 MET cc_start: 0.9034 (mmm) cc_final: 0.8722 (mmm)
REVERT: B  228 ASP cc_start: 0.8385 (m-30) cc_final: 0.7902 (m-30)
REVERT: G   18 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6861 (tm-30)
REVERT: S    3 GLN cc_start: 0.8145 (tp40) cc_final: 0.7729 (tt0)
REVERT: S  141 GLU cc_start: 0.8179 (mp0) cc_final: 0.7655 (mp0)
REVERT: S  180 MET cc_start: 0.8724 (ptm) cc_final: 0.8030 (ptm)
  outliers start: 31
  outliers final: 12
  residues processed: 264
  average time/residue: 0.2512
  time to fit residues: 91.0051
Evaluate side-chains
  211 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 197
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
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 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 G residue   16 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  226 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 0 optimal weight:   50.0000
   chunk 126 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:   50.0000
   chunk 99 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0010
   overall best weight:    1.1790

-------------------------------------------------------------------------------
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
** A 331 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 = 0.3757 r_free = 0.3757 target = 0.141138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.097184 restraints weight = 16706.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.100003 restraints weight = 9097.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.101893 restraints weight = 6135.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10439  Z= 0.140
  Angle     :  0.627  11.002  14158  Z= 0.316
  Chirality :  0.041   0.158   1572
  Planarity :  0.004   0.062   1801
  Dihedral  :  5.881  55.592   1477
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.23), residues: 1283
  helix:  0.91 (0.25), residues: 431
  sheet: -2.69 (0.29), residues: 246
  loop : -2.14 (0.23), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 480 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.013   0.001   PHE R 318 
 TYR   0.013   0.001   TYR A 296 
 ARG   0.005   0.000   ARG R 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  428)
  hydrogen bonds       : angle       4.82381 ( 1221)
  SS BOND              : bond        0.00367 (   12)
  SS BOND              : angle       1.29004 (   24)
  covalent geometry    : bond        0.00322 (10427)
  covalent geometry    : angle       0.62572 (14134)

*********************** 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
  250 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  237 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8136 (t80)
REVERT: R  246 LEU cc_start: 0.8992 (tp) cc_final: 0.8740 (mt)
REVERT: R  261 ARG cc_start: 0.6841 (ptt-90) cc_final: 0.6547 (mtm-85)
REVERT: R  301 MET cc_start: 0.8616 (ptp) cc_final: 0.8378 (ptp)
REVERT: R  339 TRP cc_start: 0.9005 (m-10) cc_final: 0.8185 (m-90)
REVERT: R  397 TYR cc_start: 0.8041 (p90) cc_final: 0.7714 (p90)
REVERT: R  475 PHE cc_start: 0.6232 (m-80) cc_final: 0.5538 (m-10)
REVERT: R  481 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7645 (tp30)
REVERT: A  331 ASN cc_start: 0.8539 (m-40) cc_final: 0.8221 (p0)
REVERT: B   15 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8950 (mtpt)
REVERT: B   82 TRP cc_start: 0.9204 (m100) cc_final: 0.8526 (m100)
REVERT: B   95 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8846 (pp)
REVERT: B  188 MET cc_start: 0.9030 (mmm) cc_final: 0.8720 (mmm)
REVERT: B  339 TRP cc_start: 0.8917 (m100) cc_final: 0.8711 (m100)
REVERT: S  128 MET cc_start: 0.8285 (mmm) cc_final: 0.7635 (mmm)
REVERT: S  141 GLU cc_start: 0.8165 (mp0) cc_final: 0.7693 (mp0)
REVERT: S  160 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8770 (p)
REVERT: S  180 MET cc_start: 0.8649 (ptm) cc_final: 0.8002 (ptm)
  outliers start: 40
  outliers final: 19
  residues processed: 236
  average time/residue: 0.2451
  time to fit residues: 81.3840
Evaluate side-chains
  210 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 PHE
Chi-restraints excluded: chain R residue  241 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  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 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 106 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   chunk 11 optimal weight:   20.0000
   chunk 115 optimal weight:    0.2980
   chunk 22 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 126 optimal weight:    4.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
G  59 ASN
S 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.140764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.104149 restraints weight = 16561.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103678 restraints weight = 10901.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.104269 restraints weight = 10494.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10439  Z= 0.155
  Angle     :  0.627  11.451  14158  Z= 0.315
  Chirality :  0.041   0.161   1572
  Planarity :  0.004   0.060   1801
  Dihedral  :  5.795  55.399   1477
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 16.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.23), residues: 1283
  helix:  1.12 (0.25), residues: 432
  sheet: -2.51 (0.29), residues: 245
  loop : -2.07 (0.23), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP R 119 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.013   0.001   PHE R 318 
 TYR   0.017   0.001   TYR A 296 
 ARG   0.008   0.000   ARG R 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03817 (  428)
  hydrogen bonds       : angle       4.71667 ( 1221)
  SS BOND              : bond        0.00357 (   12)
  SS BOND              : angle       1.13234 (   24)
  covalent geometry    : bond        0.00361 (10427)
  covalent geometry    : angle       0.62574 (14134)

*********************** 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
  259 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 210
  time to evaluate  : 2.593 
Fit side-chains
   revert: symmetry clash
REVERT: R  237 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8148 (t80)
REVERT: R  246 LEU cc_start: 0.8971 (tp) cc_final: 0.8738 (mt)
REVERT: R  261 ARG cc_start: 0.6902 (ptt-90) cc_final: 0.6606 (mtm-85)
REVERT: R  339 TRP cc_start: 0.9050 (m-10) cc_final: 0.8240 (m-90)
REVERT: R  397 TYR cc_start: 0.8061 (p90) cc_final: 0.7736 (p90)
REVERT: A  277 LYS cc_start: 0.8898 (tptt) cc_final: 0.8654 (tppt)
REVERT: B   15 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8964 (mtpt)
REVERT: B   59 TYR cc_start: 0.9200 (m-80) cc_final: 0.8787 (m-80)
REVERT: B   61 MET cc_start: 0.7838 (ttm) cc_final: 0.7630 (ttm)
REVERT: B   82 TRP cc_start: 0.9242 (m100) cc_final: 0.9009 (m100)
REVERT: B  138 GLU cc_start: 0.7357 (pp20) cc_final: 0.6982 (pp20)
REVERT: B  188 MET cc_start: 0.9007 (mmm) cc_final: 0.8661 (mmm)
REVERT: G   21 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6945 (tmm)
REVERT: G   48 ASP cc_start: 0.9014 (t0) cc_final: 0.8777 (t0)
REVERT: S  128 MET cc_start: 0.8387 (mmm) cc_final: 0.7816 (mmm)
REVERT: S  141 GLU cc_start: 0.8153 (mp0) cc_final: 0.7678 (mp0)
REVERT: S  180 MET cc_start: 0.8668 (ptm) cc_final: 0.7981 (ptm)
REVERT: S  208 GLU cc_start: 0.8097 (pm20) cc_final: 0.6892 (pm20)
  outliers start: 49
  outliers final: 30
  residues processed: 240
  average time/residue: 0.2953
  time to fit residues: 101.6775
Evaluate side-chains
  225 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 1.757 
-------------------------------------------------------------------------------
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  237 PHE
Chi-restraints excluded: chain R residue  241 THR
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  458 LEU
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  160 SER
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 B residue  273 ILE
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  129 THR
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 120 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
R 180 ASN
R 511 ASN
A 256 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.140560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.096452 restraints weight = 16406.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.099243 restraints weight = 8927.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.101091 restraints weight = 6096.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10439  Z= 0.159
  Angle     :  0.634  11.505  14158  Z= 0.318
  Chirality :  0.041   0.162   1572
  Planarity :  0.004   0.058   1801
  Dihedral  :  5.734  53.410   1477
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 17.24 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.23), residues: 1283
  helix:  1.28 (0.25), residues: 431
  sheet: -2.43 (0.29), residues: 247
  loop : -2.07 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 297 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.013   0.001   PHE R 318 
 TYR   0.019   0.001   TYR A 296 
 ARG   0.005   0.000   ARG R 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  428)
  hydrogen bonds       : angle       4.64757 ( 1221)
  SS BOND              : bond        0.00445 (   12)
  SS BOND              : angle       1.94084 (   24)
  covalent geometry    : bond        0.00372 (10427)
  covalent geometry    : angle       0.62949 (14134)

*********************** 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
  250 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 201
  time to evaluate  : 1.913 
Fit side-chains
   revert: symmetry clash
REVERT: R  237 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8103 (t80)
REVERT: R  246 LEU cc_start: 0.8983 (tp) cc_final: 0.8734 (mt)
REVERT: R  261 ARG cc_start: 0.6920 (ptt-90) cc_final: 0.6584 (mtm-85)
REVERT: R  339 TRP cc_start: 0.8984 (m-10) cc_final: 0.8148 (m-90)
REVERT: R  397 TYR cc_start: 0.8015 (p90) cc_final: 0.7687 (p90)
REVERT: R  454 ILE cc_start: 0.8346 (mt) cc_final: 0.8020 (mt)
REVERT: R  475 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5911 (m-80)
REVERT: A  277 LYS cc_start: 0.8917 (tptt) cc_final: 0.8614 (tppt)
REVERT: B   15 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8973 (mtpt)
REVERT: B   36 ASN cc_start: 0.9010 (t0) cc_final: 0.8748 (t0)
REVERT: B  138 GLU cc_start: 0.7557 (pp20) cc_final: 0.7180 (pp20)
REVERT: B  188 MET cc_start: 0.9010 (mmm) cc_final: 0.8713 (mmm)
REVERT: G   21 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6839 (tmm)
REVERT: S  128 MET cc_start: 0.8381 (mmm) cc_final: 0.7706 (mmm)
REVERT: S  141 GLU cc_start: 0.8140 (mp0) cc_final: 0.7690 (mp0)
REVERT: S  160 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8785 (p)
REVERT: S  180 MET cc_start: 0.8717 (ptm) cc_final: 0.7999 (ptm)
  outliers start: 49
  outliers final: 32
  residues processed: 233
  average time/residue: 0.2520
  time to fit residues: 84.4879
Evaluate side-chains
  226 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 190
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
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  237 PHE
Chi-restraints excluded: chain R residue  241 THR
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  458 LEU
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
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  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  157 ILE
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  177 THR
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 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  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 63 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0570
   chunk 51 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.144621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.106981 restraints weight = 16606.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.106149 restraints weight = 11128.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.106927 restraints weight = 10723.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10439  Z= 0.119
  Angle     :  0.620  11.691  14158  Z= 0.309
  Chirality :  0.041   0.213   1572
  Planarity :  0.004   0.055   1801
  Dihedral  :  5.525  50.537   1477
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.51 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.23), residues: 1283
  helix:  1.42 (0.25), residues: 431
  sheet: -2.30 (0.31), residues: 237
  loop : -1.99 (0.24), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 297 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.011   0.001   PHE R 318 
 TYR   0.019   0.001   TYR A 302 
 ARG   0.005   0.000   ARG R 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  428)
  hydrogen bonds       : angle       4.53175 ( 1221)
  SS BOND              : bond        0.00352 (   12)
  SS BOND              : angle       1.70074 (   24)
  covalent geometry    : bond        0.00272 (10427)
  covalent geometry    : angle       0.61614 (14134)

*********************** 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
  252 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 209
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  246 LEU cc_start: 0.8916 (tp) cc_final: 0.8692 (mt)
REVERT: R  261 ARG cc_start: 0.6771 (ptt-90) cc_final: 0.6551 (mtm-85)
REVERT: R  339 TRP cc_start: 0.8995 (m-10) cc_final: 0.8208 (m-90)
REVERT: R  397 TYR cc_start: 0.8020 (p90) cc_final: 0.7706 (p90)
REVERT: R  420 ILE cc_start: 0.7524 (mm) cc_final: 0.7165 (mm)
REVERT: R  454 ILE cc_start: 0.8388 (mt) cc_final: 0.8061 (mt)
REVERT: R  475 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5759 (m-80)
REVERT: A  277 LYS cc_start: 0.8832 (tptt) cc_final: 0.8559 (tppt)
REVERT: B   15 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8995 (mtpt)
REVERT: B   36 ASN cc_start: 0.9100 (t0) cc_final: 0.8851 (t0)
REVERT: B   59 TYR cc_start: 0.9231 (m-80) cc_final: 0.8586 (m-80)
REVERT: B   82 TRP cc_start: 0.9249 (m100) cc_final: 0.8521 (m100)
REVERT: B  138 GLU cc_start: 0.7629 (pp20) cc_final: 0.7222 (pp20)
REVERT: B  188 MET cc_start: 0.8977 (mmm) cc_final: 0.8639 (mmm)
REVERT: G   21 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6834 (tmm)
REVERT: S   68 PHE cc_start: 0.8361 (m-10) cc_final: 0.7956 (m-80)
REVERT: S  128 MET cc_start: 0.8282 (mmm) cc_final: 0.7633 (mmm)
REVERT: S  141 GLU cc_start: 0.8147 (mp0) cc_final: 0.7674 (mp0)
REVERT: S  180 MET cc_start: 0.8604 (ptm) cc_final: 0.7962 (ptm)
  outliers start: 43
  outliers final: 32
  residues processed: 234
  average time/residue: 0.2157
  time to fit residues: 71.6462
Evaluate side-chains
  225 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
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  392 VAL
Chi-restraints excluded: chain R residue  426 LEU
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  490 CYS
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  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  157 ILE
Chi-restraints excluded: chain B residue  160 SER
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 B residue  273 ILE
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  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:   50.0000
   chunk 9 optimal weight:    0.0020
   chunk 35 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0000
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 85 optimal weight:    6.9990
   chunk 126 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.4994

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.146193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.108722 restraints weight = 16821.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108166 restraints weight = 11037.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109382 restraints weight = 10665.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10439  Z= 0.114
  Angle     :  0.618  10.691  14158  Z= 0.310
  Chirality :  0.041   0.202   1572
  Planarity :  0.004   0.104   1801
  Dihedral  :  5.417  48.843   1477
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.05 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.24), residues: 1283
  helix:  1.48 (0.25), residues: 432
  sheet: -2.16 (0.31), residues: 239
  loop : -1.95 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 297 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.016   0.001   PHE R 526 
 TYR   0.012   0.001   TYR A 230 
 ARG   0.004   0.000   ARG R 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  428)
  hydrogen bonds       : angle       4.47245 ( 1221)
  SS BOND              : bond        0.00567 (   12)
  SS BOND              : angle       1.53626 (   24)
  covalent geometry    : bond        0.00256 (10427)
  covalent geometry    : angle       0.61552 (14134)

*********************** 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
  254 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 207
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  261 ARG cc_start: 0.6719 (ptt-90) cc_final: 0.6506 (mtm-85)
REVERT: R  339 TRP cc_start: 0.8985 (m-10) cc_final: 0.8202 (m-90)
REVERT: R  366 SER cc_start: 0.8495 (m) cc_final: 0.8238 (m)
REVERT: R  397 TYR cc_start: 0.7954 (p90) cc_final: 0.7679 (p90)
REVERT: R  454 ILE cc_start: 0.8379 (mt) cc_final: 0.8050 (mt)
REVERT: R  475 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.5305 (m-10)
REVERT: A   51 LYS cc_start: 0.8794 (pttp) cc_final: 0.8552 (tptt)
REVERT: B   59 TYR cc_start: 0.9106 (m-80) cc_final: 0.8637 (m-80)
REVERT: B   82 TRP cc_start: 0.9229 (m100) cc_final: 0.8492 (m100)
REVERT: B  114 CYS cc_start: 0.8632 (t) cc_final: 0.8267 (t)
REVERT: B  138 GLU cc_start: 0.7639 (pp20) cc_final: 0.7240 (pp20)
REVERT: B  188 MET cc_start: 0.8935 (mmm) cc_final: 0.8627 (mmm)
REVERT: G   21 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6844 (tmm)
REVERT: S   68 PHE cc_start: 0.8283 (m-10) cc_final: 0.7805 (m-80)
REVERT: S  128 MET cc_start: 0.8213 (mmm) cc_final: 0.7582 (mmm)
REVERT: S  141 GLU cc_start: 0.8162 (mp0) cc_final: 0.7760 (mp0)
REVERT: S  180 MET cc_start: 0.8559 (ptm) cc_final: 0.7916 (ptm)
  outliers start: 47
  outliers final: 30
  residues processed: 239
  average time/residue: 0.2352
  time to fit residues: 81.7558
Evaluate side-chains
  222 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
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  234 ILE
Chi-restraints excluded: chain R residue  314 CYS
Chi-restraints excluded: chain R residue  317 ILE
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  490 CYS
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   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  157 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  277 SER
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  226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN
S 155 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108247 restraints weight = 16642.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.107583 restraints weight = 11077.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.108857 restraints weight = 10245.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10439  Z= 0.127
  Angle     :  0.632  12.351  14158  Z= 0.316
  Chirality :  0.041   0.180   1572
  Planarity :  0.004   0.104   1801
  Dihedral  :  5.362  46.703   1477
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.33 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.24), residues: 1283
  helix:  1.40 (0.26), residues: 441
  sheet: -2.08 (0.31), residues: 244
  loop : -1.93 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 297 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.019   0.001   PHE R 237 
 TYR   0.017   0.001   TYR R 472 
 ARG   0.004   0.000   ARG R 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  428)
  hydrogen bonds       : angle       4.51138 ( 1221)
  SS BOND              : bond        0.00326 (   12)
  SS BOND              : angle       1.59645 (   24)
  covalent geometry    : bond        0.00293 (10427)
  covalent geometry    : angle       0.62917 (14134)

*********************** 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
  242 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 198
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  261 ARG cc_start: 0.6774 (ptt-90) cc_final: 0.6556 (mtm-85)
REVERT: R  339 TRP cc_start: 0.8990 (m-10) cc_final: 0.8189 (m-90)
REVERT: R  366 SER cc_start: 0.8517 (m) cc_final: 0.8251 (m)
REVERT: R  454 ILE cc_start: 0.8382 (mt) cc_final: 0.8126 (mt)
REVERT: R  475 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5716 (m-80)
REVERT: A   51 LYS cc_start: 0.8785 (pttp) cc_final: 0.8556 (tptt)
REVERT: A  277 LYS cc_start: 0.8849 (tptt) cc_final: 0.8596 (tppt)
REVERT: A  302 TYR cc_start: 0.8654 (t80) cc_final: 0.8323 (t80)
REVERT: B   59 TYR cc_start: 0.9108 (m-80) cc_final: 0.8881 (m-80)
REVERT: B   82 TRP cc_start: 0.9209 (m100) cc_final: 0.8521 (m100)
REVERT: B  138 GLU cc_start: 0.7654 (pp20) cc_final: 0.7219 (pp20)
REVERT: B  188 MET cc_start: 0.8958 (mmm) cc_final: 0.8649 (mmm)
REVERT: G   21 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6834 (tmm)
REVERT: S   68 PHE cc_start: 0.8276 (m-10) cc_final: 0.7752 (m-80)
REVERT: S  128 MET cc_start: 0.8187 (mmm) cc_final: 0.7542 (mmm)
REVERT: S  141 GLU cc_start: 0.8185 (mp0) cc_final: 0.7788 (mp0)
REVERT: S  180 MET cc_start: 0.8473 (ptm) cc_final: 0.7864 (ptm)
  outliers start: 44
  outliers final: 35
  residues processed: 231
  average time/residue: 0.3763
  time to fit residues: 122.6872
Evaluate side-chains
  223 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 186
  time to evaluate  : 2.269 
-------------------------------------------------------------------------------
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  241 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  490 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   47 THR
Chi-restraints excluded: chain B residue   61 MET
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  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  277 SER
Chi-restraints excluded: chain B residue  296 VAL
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 127 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 93 optimal weight:    0.0070
   chunk 118 optimal weight:    0.0870
   chunk 33 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.110737 restraints weight = 16696.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109267 restraints weight = 12352.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.110649 restraints weight = 11620.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10439  Z= 0.115
  Angle     :  0.644  11.831  14158  Z= 0.318
  Chirality :  0.041   0.177   1572
  Planarity :  0.004   0.100   1801
  Dihedral  :  5.219  45.397   1477
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.23 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.24), residues: 1283
  helix:  1.43 (0.25), residues: 441
  sheet: -1.94 (0.31), residues: 245
  loop : -1.87 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 211 
 HIS   0.007   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 237 
 TYR   0.020   0.001   TYR A 230 
 ARG   0.003   0.000   ARG R 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  428)
  hydrogen bonds       : angle       4.47779 ( 1221)
  SS BOND              : bond        0.00479 (   12)
  SS BOND              : angle       1.63630 (   24)
  covalent geometry    : bond        0.00260 (10427)
  covalent geometry    : angle       0.64057 (14134)

*********************** 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
  240 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 202
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  339 TRP cc_start: 0.8948 (m-10) cc_final: 0.8168 (m-90)
REVERT: R  366 SER cc_start: 0.8534 (m) cc_final: 0.8267 (m)
REVERT: R  454 ILE cc_start: 0.8431 (mt) cc_final: 0.8000 (mt)
REVERT: R  475 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.5173 (m-10)
REVERT: A  243 MET cc_start: 0.7981 (mmp) cc_final: 0.7623 (mmp)
REVERT: A  277 LYS cc_start: 0.8841 (tptt) cc_final: 0.8571 (tppt)
REVERT: A  302 TYR cc_start: 0.8593 (t80) cc_final: 0.8280 (t80)
REVERT: B   82 TRP cc_start: 0.9179 (m100) cc_final: 0.8730 (m100)
REVERT: B  138 GLU cc_start: 0.7727 (pp20) cc_final: 0.7346 (pp20)
REVERT: B  188 MET cc_start: 0.8955 (mmm) cc_final: 0.8670 (mmm)
REVERT: G   21 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6829 (tmm)
REVERT: S   68 PHE cc_start: 0.8283 (m-10) cc_final: 0.7802 (m-80)
REVERT: S  128 MET cc_start: 0.8203 (mmm) cc_final: 0.7563 (mmm)
REVERT: S  141 GLU cc_start: 0.8152 (mp0) cc_final: 0.7754 (mp0)
REVERT: S  180 MET cc_start: 0.8403 (ptm) cc_final: 0.7808 (ptm)
  outliers start: 38
  outliers final: 31
  residues processed: 230
  average time/residue: 0.2137
  time to fit residues: 69.5261
Evaluate side-chains
  218 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
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  241 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  467 PHE
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  490 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   47 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   78 LYS
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 104 optimal weight:    0.0000
   chunk 40 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 100 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   chunk 47 optimal weight:    0.5980
   chunk 124 optimal weight:    8.9990
   overall best weight:    1.6988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.144148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107153 restraints weight = 16834.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.106074 restraints weight = 11788.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.107069 restraints weight = 11655.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10439  Z= 0.171
  Angle     :  0.683  11.721  14158  Z= 0.342
  Chirality :  0.043   0.233   1572
  Planarity :  0.005   0.100   1801
  Dihedral  :  5.217  45.600   1475
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 22.32 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.23), residues: 1283
  helix:  1.38 (0.25), residues: 441
  sheet: -2.13 (0.30), residues: 244
  loop : -1.88 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP B 297 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R 237 
 TYR   0.023   0.001   TYR A 230 
 ARG   0.008   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  428)
  hydrogen bonds       : angle       4.59617 ( 1221)
  SS BOND              : bond        0.00599 (   12)
  SS BOND              : angle       1.85192 (   24)
  covalent geometry    : bond        0.00400 (10427)
  covalent geometry    : angle       0.67920 (14134)

********************** 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
  221 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 186
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  339 TRP cc_start: 0.9039 (m-10) cc_final: 0.8460 (m-10)
REVERT: R  366 SER cc_start: 0.8541 (m) cc_final: 0.8285 (m)
REVERT: R  454 ILE cc_start: 0.8530 (mt) cc_final: 0.8117 (mt)
REVERT: R  475 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5774 (m-80)
REVERT: A  277 LYS cc_start: 0.8871 (tptt) cc_final: 0.8625 (tppt)
REVERT: B   82 TRP cc_start: 0.9280 (m100) cc_final: 0.8593 (m100)
REVERT: B  138 GLU cc_start: 0.7851 (pp20) cc_final: 0.7514 (pp20)
REVERT: B  188 MET cc_start: 0.8955 (mmm) cc_final: 0.8615 (mmm)
REVERT: G   21 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6874 (tmm)
REVERT: S   68 PHE cc_start: 0.8358 (m-10) cc_final: 0.7859 (m-80)
REVERT: S  128 MET cc_start: 0.8310 (mmm) cc_final: 0.7631 (mmm)
REVERT: S  141 GLU cc_start: 0.8204 (mp0) cc_final: 0.7787 (mp0)
REVERT: S  180 MET cc_start: 0.8534 (ptm) cc_final: 0.7967 (ptm)
  outliers start: 35
  outliers final: 31
  residues processed: 213
  average time/residue: 0.2111
  time to fit residues: 64.4563
Evaluate side-chains
  216 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 183
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
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  467 PHE
Chi-restraints excluded: chain R residue  469 CYS
Chi-restraints excluded: chain R residue  475 PHE
Chi-restraints excluded: chain R residue  490 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   47 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  177 THR
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 81 optimal weight:    0.2980
   chunk 127 optimal weight:    0.1980
   chunk 36 optimal weight:    0.6980
   chunk 100 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.148113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.110774 restraints weight = 16730.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110056 restraints weight = 12174.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110847 restraints weight = 11518.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10439  Z= 0.118
  Angle     :  0.661  11.528  14158  Z= 0.327
  Chirality :  0.042   0.199   1572
  Planarity :  0.005   0.097   1801
  Dihedral  :  5.070  43.710   1475
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.69 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.24), residues: 1283
  helix:  1.45 (0.25), residues: 442
  sheet: -1.94 (0.30), residues: 247
  loop : -1.78 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 211 
 HIS   0.008   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 237 
 TYR   0.024   0.001   TYR A 230 
 ARG   0.007   0.000   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03512 (  428)
  hydrogen bonds       : angle       4.51157 ( 1221)
  SS BOND              : bond        0.00421 (   12)
  SS BOND              : angle       1.45159 (   24)
  covalent geometry    : bond        0.00267 (10427)
  covalent geometry    : angle       0.65841 (14134)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4079.69 seconds
wall clock time: 74 minutes 0.26 seconds (4440.26 seconds total)