Starting phenix.real_space_refine
on Tue Mar  3 18:29:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vvn_32145/03_2026/7vvn_32145.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vvn_32145/03_2026/7vvn_32145.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2026/7vvn_32145.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2026/7vvn_32145.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2026/7vvn_32145.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vvn_32145/03_2026/7vvn_32145.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      47      5.16       5
     C    5147      2.51       5
     N    1427      2.21       5
     O    1509      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8130
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1845
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'ASP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "B"
      Number of atoms: 2544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2544
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 43
    Chain: "G"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 410
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "N"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "P"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 196
          Classifications: {'peptide': 34}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'TRANS': 33}
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'PHE%COO:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "R"
      Number of atoms: 2169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2169
          Classifications: {'peptide': 300}
          Incomplete info: {'truncation_to_alanine': 73}
          Link IDs: {'PTRANS': 6, 'TRANS': 293}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 363
          Unresolved non-hydrogen angles: 471
          Unresolved non-hydrogen dihedrals: 337
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 5, 'HIS:plan': 5, 'ARG:plan': 9, 'TRP:plan': 5, 'ASP:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 252
  Time building chain proxies: 1.97, per 1000 atoms: 0.24
  Number of scatterers: 8130
  At special positions: 0
  Unit cell: (123.947, 105.134, 115.094, 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      47     16.00
     O    1509      8.00
     N    1427      7.00
     C    5147      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.09
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 325.6 milliseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 11 sheets defined
      41.5% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.864A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.502A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.549A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 3.875A  pdb=" N   GLN A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   GLU A 258 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
      removed outlier: 3.557A  pdb=" N   GLU A 289 " --> pdb=" O   ASP A 285 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LEU A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.135A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.548A  pdb=" N   ARG A 307 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 343
      removed outlier: 3.572A  pdb=" N   ALA A 327 " --> pdb=" O   ARG A 323 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ARG A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLY A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 382
      removed outlier: 3.574A  pdb=" N   GLN A 380 " --> pdb=" O   MET A 376 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A 381 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.730A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 4.013A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.545A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.004A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR G  40 " --> pdb=" O   ASP G  36 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 15
    Processing helix  chain 'P' and resid 16 through 19
      removed outlier: 4.105A  pdb=" N   GLU P  19 " --> pdb=" O   ASN P  16 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 16 through 19'
    Processing helix  chain 'P' and resid 20 through 34
    Processing helix  chain 'R' and resid 34 through 49
    Processing helix  chain 'R' and resid 182 through 207
      removed outlier: 3.634A  pdb=" N   GLY R 188 " --> pdb=" O   PHE R 184 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   MET R 189 " --> pdb=" O   ASP R 185 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ILE R 190 " --> pdb=" O   ARG R 186 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR R 191 " --> pdb=" O   LEU R 187 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLY R 194 " --> pdb=" O   ILE R 190 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU R 207 " --> pdb=" O   THR R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 211
    Processing helix  chain 'R' and resid 219 through 244
      removed outlier: 3.596A  pdb=" N   MET R 224 " --> pdb=" O   ASN R 220 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   HIS R 225 " --> pdb=" O   TYR R 221 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE R 238 " --> pdb=" O   ALA R 234 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS R 240 " --> pdb=" O   SER R 236 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASP R 241 " --> pdb=" O   ILE R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 312
      removed outlier: 3.900A  pdb=" N   LEU R 300 " --> pdb=" O   TYR R 296 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER R 308 " --> pdb=" O   LEU R 304 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET R 312 " --> pdb=" O   SER R 308 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 326
    Processing helix  chain 'R' and resid 329 through 346
      removed outlier: 3.758A  pdb=" N   ALA R 333 " --> pdb=" O   TRP R 329 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL R 338 " --> pdb=" O   VAL R 334 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TRP R 339 " --> pdb=" O   PHE R 335 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER R 341 " --> pdb=" O   ALA R 337 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL R 342 " --> pdb=" O   VAL R 338 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 364 through 379
    Processing helix  chain 'R' and resid 381 through 391
      removed outlier: 3.704A  pdb=" N   LEU R 385 " --> pdb=" O   ILE R 381 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG R 390 " --> pdb=" O   ALA R 386 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLU R 391 " --> pdb=" O   THR R 387 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 401 through 413
      removed outlier: 3.656A  pdb=" N   LEU R 407 " --> pdb=" O   TYR R 403 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL R 412 " --> pdb=" O   LYS R 408 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 418 through 420
      No H-bonds generated for 'chain 'R' and resid 418 through 420'
    Processing helix  chain 'R' and resid 421 through 426
      removed outlier: 4.589A  pdb=" N   ALA R 426 " --> pdb=" O   ILE R 422 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 437 through 451
      removed outlier: 3.754A  pdb=" N   GLU R 444 " --> pdb=" O   GLN R 440 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 452 through 454
      No H-bonds generated for 'chain 'R' and resid 452 through 454'
    Processing helix  chain 'R' and resid 455 through 461
    Processing helix  chain 'R' and resid 463 through 480
      removed outlier: 3.710A  pdb=" N   LYS R 472 " --> pdb=" O   ALA R 468 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER R 475 " --> pdb=" O   LYS R 471 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ALA R 480 " --> pdb=" O   ARG R 476 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.712A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210
      removed outlier: 5.903A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.577A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 7.242A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.521A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.482A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.610A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.912A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320
      removed outlier: 3.550A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.514A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU N  79 " --> pdb=" O   CYS N  22 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12
      removed outlier: 7.152A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    353 hydrogen bonds defined for protein.
    996 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1368
        1.32 -     1.45: 2255
        1.45 -     1.57: 4593
        1.57 -     1.70: 0
        1.70 -     1.83: 66
  Bond restraints: 8282
  Sorted by residual:
  bond pdb=" CA  SER B  97 "
       pdb=" CB  SER B  97 "
    ideal  model  delta    sigma   weight residual
    1.526  1.461  0.066 1.53e-02 4.27e+03 1.85e+01
  bond pdb=" N   VAL R 455 "
       pdb=" CA  VAL R 455 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.06e-02 8.90e+03 1.44e+01
  bond pdb=" C   SER B  72 "
       pdb=" O   SER B  72 "
    ideal  model  delta    sigma   weight residual
    1.234  1.188  0.046 1.22e-02 6.72e+03 1.42e+01
  bond pdb=" N   HIS R 420 "
       pdb=" CA  HIS R 420 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.23e-02 6.61e+03 1.26e+01
  bond pdb=" CA  SER B 160 "
       pdb=" CB  SER B 160 "
    ideal  model  delta    sigma   weight residual
    1.531  1.478  0.052 1.52e-02 4.33e+03 1.19e+01
  ... (remaining 8277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 6672
        1.51 -     3.01: 3549
        3.01 -     4.52: 927
        4.52 -     6.02: 97
        6.02 -     7.53: 6
  Bond angle restraints: 11251
  Sorted by residual:
  angle pdb=" CA  PHE R 335 "
        pdb=" CB  PHE R 335 "
        pdb=" CG  PHE R 335 "
      ideal   model   delta    sigma   weight residual
     113.80  108.42    5.38 1.00e+00 1.00e+00 2.90e+01
  angle pdb=" C   GLU B 130 "
        pdb=" N   GLY B 131 "
        pdb=" CA  GLY B 131 "
      ideal   model   delta    sigma   weight residual
     119.98  125.38   -5.40 1.11e+00 8.12e-01 2.37e+01
  angle pdb=" C   ASP A 215 "
        pdb=" CA  ASP A 215 "
        pdb=" CB  ASP A 215 "
      ideal   model   delta    sigma   weight residual
     111.80  118.72   -6.92 1.46e+00 4.69e-01 2.25e+01
  angle pdb=" CA  ILE R 381 "
        pdb=" C   ILE R 381 "
        pdb=" O   ILE R 381 "
      ideal   model   delta    sigma   weight residual
     119.29  115.44    3.85 8.40e-01 1.42e+00 2.10e+01
  angle pdb=" CA  ARG A 231 "
        pdb=" C   ARG A 231 "
        pdb=" O   ARG A 231 "
      ideal   model   delta    sigma   weight residual
     121.34  116.02    5.32 1.18e+00 7.18e-01 2.04e+01
  ... (remaining 11246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4351
       17.93 -    35.85: 444
       35.85 -    53.78: 69
       53.78 -    71.71: 15
       71.71 -    89.63: 9
  Dihedral angle restraints: 4888
    sinusoidal: 1738
      harmonic: 3150
  Sorted by residual:
  dihedral pdb=" CA  PHE R 314 "
           pdb=" C   PHE R 314 "
           pdb=" N   PHE R 315 "
           pdb=" CA  PHE R 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.75   27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  LEU B 190 "
           pdb=" C   LEU B 190 "
           pdb=" N   SER B 191 "
           pdb=" CA  SER B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.83   27.17     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.72   25.28     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 4885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 601
       0.057 -    0.113: 463
       0.113 -    0.170: 189
       0.170 -    0.226: 44
       0.226 -    0.283: 4
  Chirality restraints: 1301
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CB  ILE B 338 "
            pdb=" CA  ILE B 338 "
            pdb=" CG1 ILE B 338 "
            pdb=" CG2 ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CB  ILE B 229 "
            pdb=" CA  ILE B 229 "
            pdb=" CG1 ILE B 229 "
            pdb=" CG2 ILE B 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1298 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 335 "   -0.046 2.00e-02 2.50e+03   3.20e-02 1.80e+01
        pdb=" CG  PHE R 335 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 335 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 335 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 335 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 335 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 335 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.034 2.00e-02 2.50e+03   2.42e-02 1.18e+01
        pdb=" CG  TYR B  59 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 339 "   -0.032 2.00e-02 2.50e+03   1.90e-02 9.06e+00
        pdb=" CG  TRP B 339 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 339 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 339 "   -0.017 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 339 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 339 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 339 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 339 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 339 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 339 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 377
        2.73 -     3.27: 8411
        3.27 -     3.81: 12432
        3.81 -     4.36: 16717
        4.36 -     4.90: 26899
  Nonbonded interactions: 64836
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   SER N  30 "
            pdb=" NE2 GLN N  53 "
     model   vdw
     2.286 3.120
  ... (remaining 64831 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:             0.220
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.410
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
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      :  0.013   0.066   8286  Z= 0.989
  Angle     :  1.783  10.327  11259  Z= 1.314
  Chirality :  0.084   0.283   1301
  Planarity :  0.006   0.032   1446
  Dihedral  : 15.145  89.634   2828
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.07 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  7.49 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.23), residues: 1054
  helix: -0.50 (0.24), residues: 388
  sheet: -2.25 (0.31), residues: 176
  loop : -1.91 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG N  72 
 TYR   0.058   0.007   TYR B  59 
 PHE   0.068   0.006   PHE R 335 
 TRP   0.032   0.007   TRP B 339 
 HIS   0.023   0.005   HIS R 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.01332 ( 8282)
  covalent geometry    : angle       1.78041 (11251)
  SS BOND              : bond        0.03102 (    4)
  SS BOND              : angle       4.16015 (    8)
  hydrogen bonds       : bond        0.27559 (  349)
  hydrogen bonds       : angle       9.11007 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.4218 (mm-40) cc_final: 0.4009 (mm110)
REVERT: A   27 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6850 (mm-30)
REVERT: A   28 LYS cc_start: 0.8166 (tttm) cc_final: 0.7740 (ttmt)
REVERT: A   34 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7383 (tmtt)
REVERT: A   38 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8350 (mmm-85)
REVERT: A  230 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8275 (mp0)
REVERT: A  270 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7900 (ttm110)
REVERT: A  284 GLN cc_start: 0.7188 (mm110) cc_final: 0.6983 (mm110)
REVERT: A  297 LYS cc_start: 0.8263 (ptpp) cc_final: 0.7867 (ptmm)
REVERT: A  360 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6658 (tp30)
REVERT: B   23 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7295 (mptt)
REVERT: B   35 ASN cc_start: 0.7926 (t0) cc_final: 0.7710 (t0)
REVERT: B   42 ARG cc_start: 0.7081 (tpm170) cc_final: 0.6450 (mmt90)
REVERT: B   52 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7252 (mmt90)
REVERT: B   82 TRP cc_start: 0.8751 (m-90) cc_final: 0.8364 (m-90)
REVERT: B   85 TYR cc_start: 0.7751 (m-80) cc_final: 0.7497 (m-80)
REVERT: B  124 TYR cc_start: 0.8483 (m-80) cc_final: 0.8081 (m-80)
REVERT: B  217 MET cc_start: 0.7585 (ppp) cc_final: 0.7220 (ppp)
REVERT: B  219 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7842 (ttp80)
REVERT: B  261 LEU cc_start: 0.7442 (mm) cc_final: 0.7094 (mp)
REVERT: B  268 ASN cc_start: 0.8492 (m-40) cc_final: 0.8183 (t0)
REVERT: B  280 LYS cc_start: 0.7070 (mmtm) cc_final: 0.5984 (ttmt)
REVERT: G   38 MET cc_start: 0.8542 (mmm) cc_final: 0.8199 (mmm)
REVERT: G   44 HIS cc_start: 0.8279 (m-70) cc_final: 0.8040 (m-70)
REVERT: N    5 GLN cc_start: 0.8055 (mt0) cc_final: 0.7835 (pm20)
REVERT: N   32 TYR cc_start: 0.8029 (m-80) cc_final: 0.7733 (m-80)
REVERT: N   39 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8165 (tp-100)
REVERT: N   80 TYR cc_start: 0.8153 (m-80) cc_final: 0.7863 (m-80)
REVERT: N   83 MET cc_start: 0.7999 (mmm) cc_final: 0.7789 (mmt)
REVERT: N   95 TYR cc_start: 0.7829 (m-80) cc_final: 0.7501 (m-80)
REVERT: R  185 ASP cc_start: 0.7416 (m-30) cc_final: 0.7149 (m-30)
REVERT: R  220 ASN cc_start: 0.7792 (m110) cc_final: 0.7457 (m-40)
REVERT: R  312 MET cc_start: 0.6686 (mmt) cc_final: 0.6148 (mtp)
REVERT: R  408 LYS cc_start: 0.7138 (tttp) cc_final: 0.6896 (tmtt)
REVERT: R  466 VAL cc_start: 0.8131 (p) cc_final: 0.7549 (m)
REVERT: R  470 ILE cc_start: 0.7897 (tt) cc_final: 0.7608 (pt)
  outliers start: 3
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1121
  time to fit residues: 30.2709
Evaluate side-chains
  139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 340 ASN
R 295 ASN
** R 374 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 = 0.3907 r_free = 0.3907 target = 0.144198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.121396 restraints weight = 13649.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123879 restraints weight = 8598.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125330 restraints weight = 6185.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.126715 restraints weight = 5004.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.127410 restraints weight = 4255.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8286  Z= 0.173
  Angle     :  0.631   7.524  11259  Z= 0.337
  Chirality :  0.042   0.145   1301
  Planarity :  0.004   0.029   1446
  Dihedral  :  5.236  39.115   1163
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.98 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.25), residues: 1054
  helix:  0.55 (0.25), residues: 408
  sheet: -1.70 (0.33), residues: 208
  loop : -1.25 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG N 105 
 TYR   0.014   0.002   TYR B 105 
 PHE   0.022   0.002   PHE R 454 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8282)
  covalent geometry    : angle       0.62987 (11251)
  SS BOND              : bond        0.00665 (    4)
  SS BOND              : angle       1.59423 (    8)
  hydrogen bonds       : bond        0.05340 (  349)
  hydrogen bonds       : angle       5.69254 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.4387 (mm-40) cc_final: 0.4142 (mm110)
REVERT: A   28 LYS cc_start: 0.6536 (tttm) cc_final: 0.6270 (ttmt)
REVERT: A  360 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7056 (tp30)
REVERT: B   23 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6703 (mmtm)
REVERT: B  219 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7810 (ttp-170)
REVERT: N   34 MET cc_start: 0.8280 (mmm) cc_final: 0.8039 (mmt)
REVERT: N   83 MET cc_start: 0.6843 (mmm) cc_final: 0.6596 (mmt)
REVERT: R  185 ASP cc_start: 0.6944 (m-30) cc_final: 0.6686 (m-30)
REVERT: R  231 MET cc_start: 0.7194 (mmt) cc_final: 0.6908 (mmp)
REVERT: R  413 LEU cc_start: 0.7174 (tt) cc_final: 0.6956 (tp)
REVERT: R  466 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7688 (t)
REVERT: R  470 ILE cc_start: 0.8134 (tt) cc_final: 0.7905 (pt)
  outliers start: 17
  outliers final: 11
  residues processed: 170
  average time/residue: 0.1032
  time to fit residues: 23.0432
Evaluate side-chains
  143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  440 GLN
Chi-restraints excluded: chain R residue  466 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
N  53 GLN
N  74 ASN
P  10 ASN
R 374 ASN
R 440 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.137286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.117950 restraints weight = 14218.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.118418 restraints weight = 11433.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.118931 restraints weight = 9098.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.119430 restraints weight = 8290.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.119650 restraints weight = 7423.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8286  Z= 0.217
  Angle     :  0.653   7.151  11259  Z= 0.349
  Chirality :  0.044   0.169   1301
  Planarity :  0.004   0.030   1446
  Dihedral  :  5.238  30.215   1159
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.10 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.25), residues: 1054
  helix:  0.62 (0.26), residues: 389
  sheet: -1.53 (0.34), residues: 197
  loop : -1.01 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 219 
 TYR   0.024   0.002   TYR B 105 
 PHE   0.031   0.002   PHE R 454 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.008   0.002   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8282)
  covalent geometry    : angle       0.65202 (11251)
  SS BOND              : bond        0.00722 (    4)
  SS BOND              : angle       1.70245 (    8)
  hydrogen bonds       : bond        0.04938 (  349)
  hydrogen bonds       : angle       5.50179 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.4696 (mm-40) cc_final: 0.4463 (mm110)
REVERT: A   38 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7688 (mmm-85)
REVERT: B    6 GLN cc_start: 0.4622 (tm-30) cc_final: 0.4063 (pt0)
REVERT: B   23 LYS cc_start: 0.7264 (mmmt) cc_final: 0.6827 (mppt)
REVERT: B  219 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7856 (ttp-170)
REVERT: N   34 MET cc_start: 0.8441 (mmm) cc_final: 0.8111 (mmt)
REVERT: R  192 THR cc_start: 0.7718 (m) cc_final: 0.7355 (p)
REVERT: R  231 MET cc_start: 0.7510 (mmt) cc_final: 0.7209 (mmp)
REVERT: R  466 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7668 (t)
  outliers start: 32
  outliers final: 22
  residues processed: 161
  average time/residue: 0.0778
  time to fit residues: 17.1819
Evaluate side-chains
  139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  365 VAL
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  466 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 76 optimal weight:   30.0000
   chunk 41 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 79 optimal weight:   20.0000
   overall best weight:    1.1742

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B 340 ASN
N  53 GLN
N  74 ASN
P  10 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.141955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.122712 restraints weight = 14444.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.122875 restraints weight = 11920.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.123913 restraints weight = 9754.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.124218 restraints weight = 8075.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.124314 restraints weight = 7328.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8286  Z= 0.119
  Angle     :  0.550   7.054  11259  Z= 0.292
  Chirality :  0.040   0.140   1301
  Planarity :  0.003   0.032   1446
  Dihedral  :  4.697  26.428   1159
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.85 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.26), residues: 1054
  helix:  0.91 (0.26), residues: 394
  sheet: -1.17 (0.34), residues: 209
  loop : -0.71 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 383 
 TYR   0.012   0.001   TYR R 459 
 PHE   0.018   0.001   PHE R 454 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8282)
  covalent geometry    : angle       0.54940 (11251)
  SS BOND              : bond        0.00468 (    4)
  SS BOND              : angle       1.12125 (    8)
  hydrogen bonds       : bond        0.04002 (  349)
  hydrogen bonds       : angle       5.04029 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 CYS cc_start: 0.7122 (p) cc_final: 0.6415 (m)
REVERT: B    6 GLN cc_start: 0.4745 (tm-30) cc_final: 0.4083 (pt0)
REVERT: B   23 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6763 (tttp)
REVERT: B   52 ARG cc_start: 0.7399 (mmt90) cc_final: 0.7092 (mtt90)
REVERT: B  205 ASP cc_start: 0.8107 (p0) cc_final: 0.7852 (p0)
REVERT: B  219 ARG cc_start: 0.8037 (mtp-110) cc_final: 0.7737 (ttt-90)
REVERT: B  261 LEU cc_start: 0.6929 (mm) cc_final: 0.6596 (mp)
REVERT: N   34 MET cc_start: 0.8337 (mmm) cc_final: 0.8107 (mmm)
REVERT: R  443 TYR cc_start: 0.7481 (t80) cc_final: 0.7207 (t80)
REVERT: R  466 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7700 (t)
  outliers start: 25
  outliers final: 17
  residues processed: 157
  average time/residue: 0.0774
  time to fit residues: 16.9235
Evaluate side-chains
  135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  444 GLU
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  474 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 71 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
B 340 ASN
N  53 GLN
N  74 ASN
P  10 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.140592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.121495 restraints weight = 14296.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.121398 restraints weight = 11991.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122362 restraints weight = 9639.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.122635 restraints weight = 8255.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.122832 restraints weight = 7627.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8286  Z= 0.148
  Angle     :  0.572   8.389  11259  Z= 0.301
  Chirality :  0.041   0.142   1301
  Planarity :  0.003   0.036   1446
  Dihedral  :  4.684  27.910   1159
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.10 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.26), residues: 1054
  helix:  0.82 (0.26), residues: 403
  sheet: -1.12 (0.34), residues: 217
  loop : -0.66 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 383 
 TYR   0.012   0.001   TYR R 459 
 PHE   0.022   0.002   PHE R 454 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8282)
  covalent geometry    : angle       0.57153 (11251)
  SS BOND              : bond        0.00573 (    4)
  SS BOND              : angle       1.30139 (    8)
  hydrogen bonds       : bond        0.04108 (  349)
  hydrogen bonds       : angle       5.00843 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7690 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6921 (p) cc_final: 0.6313 (m)
REVERT: B   23 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6892 (tttp)
REVERT: B   52 ARG cc_start: 0.7314 (mmt90) cc_final: 0.6749 (mtt90)
REVERT: B  205 ASP cc_start: 0.8168 (p0) cc_final: 0.7913 (p0)
REVERT: B  219 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7850 (ttt-90)
REVERT: B  261 LEU cc_start: 0.6794 (mm) cc_final: 0.6401 (mp)
REVERT: N   34 MET cc_start: 0.8451 (mmm) cc_final: 0.8220 (mmm)
REVERT: R  192 THR cc_start: 0.7754 (m) cc_final: 0.7364 (p)
REVERT: R  466 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7783 (t)
  outliers start: 39
  outliers final: 29
  residues processed: 157
  average time/residue: 0.0728
  time to fit residues: 16.2234
Evaluate side-chains
  148 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  444 GLU
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  474 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
N  53 GLN
N  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.140418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.120366 restraints weight = 14167.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.122244 restraints weight = 9659.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.123279 restraints weight = 7416.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.124397 restraints weight = 6266.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.124758 restraints weight = 5474.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8286  Z= 0.150
  Angle     :  0.578   8.892  11259  Z= 0.302
  Chirality :  0.040   0.143   1301
  Planarity :  0.003   0.038   1446
  Dihedral  :  4.706  34.073   1159
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 21.47 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.26), residues: 1054
  helix:  0.83 (0.26), residues: 403
  sheet: -0.99 (0.34), residues: 207
  loop : -0.76 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 337 
 TYR   0.013   0.001   TYR R 459 
 PHE   0.021   0.002   PHE R 454 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8282)
  covalent geometry    : angle       0.57742 (11251)
  SS BOND              : bond        0.00575 (    4)
  SS BOND              : angle       1.30888 (    8)
  hydrogen bonds       : bond        0.04057 (  349)
  hydrogen bonds       : angle       4.95836 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7695 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6975 (p) cc_final: 0.6393 (m)
REVERT: B   23 LYS cc_start: 0.7100 (mmmt) cc_final: 0.6713 (tttp)
REVERT: B   52 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6723 (mtt90)
REVERT: B  205 ASP cc_start: 0.8261 (p0) cc_final: 0.7991 (p0)
REVERT: B  219 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7754 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6183 (m-80)
REVERT: B  254 ASP cc_start: 0.6368 (t70) cc_final: 0.6143 (t70)
REVERT: B  261 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6271 (mp)
REVERT: R  192 THR cc_start: 0.7574 (m) cc_final: 0.7268 (p)
REVERT: R  327 PHE cc_start: 0.7390 (t80) cc_final: 0.7084 (t80)
REVERT: R  466 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7722 (t)
  outliers start: 42
  outliers final: 31
  residues processed: 158
  average time/residue: 0.0861
  time to fit residues: 18.6579
Evaluate side-chains
  153 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  444 GLU
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  474 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0570
   chunk 59 optimal weight:    9.9990
   chunk 101 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 105 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
B 340 ASN
G  18 GLN
N  74 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.144427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.125937 restraints weight = 14179.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.125934 restraints weight = 11504.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.127204 restraints weight = 9167.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127392 restraints weight = 7627.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.127530 restraints weight = 6945.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8286  Z= 0.103
  Angle     :  0.538   9.149  11259  Z= 0.278
  Chirality :  0.039   0.131   1301
  Planarity :  0.003   0.038   1446
  Dihedral  :  4.345  27.298   1159
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 23.10 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.26), residues: 1054
  helix:  1.02 (0.26), residues: 400
  sheet: -0.76 (0.35), residues: 204
  loop : -0.57 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 337 
 TYR   0.010   0.001   TYR R 459 
 PHE   0.016   0.001   PHE R 454 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8282)
  covalent geometry    : angle       0.53714 (11251)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       0.94258 (    8)
  hydrogen bonds       : bond        0.03522 (  349)
  hydrogen bonds       : angle       4.66511 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8003 (tpp80) cc_final: 0.7565 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6733 (p) cc_final: 0.6269 (m)
REVERT: B   23 LYS cc_start: 0.7145 (mmmt) cc_final: 0.6754 (tttp)
REVERT: B   45 MET cc_start: 0.7008 (mtp) cc_final: 0.6574 (mtp)
REVERT: B   52 ARG cc_start: 0.7172 (mmt90) cc_final: 0.6675 (mtt90)
REVERT: B  205 ASP cc_start: 0.8166 (p0) cc_final: 0.7865 (p0)
REVERT: B  219 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7668 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6300 (m-80)
REVERT: B  254 ASP cc_start: 0.6194 (t70) cc_final: 0.5954 (t70)
REVERT: B  261 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6426 (mp)
REVERT: P   15 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6394 (tt)
REVERT: R  220 ASN cc_start: 0.8310 (m110) cc_final: 0.8107 (m-40)
REVERT: R  231 MET cc_start: 0.7552 (mmp) cc_final: 0.7295 (mmp)
REVERT: R  237 ILE cc_start: 0.7776 (mm) cc_final: 0.7550 (tp)
REVERT: R  466 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7668 (t)
  outliers start: 32
  outliers final: 22
  residues processed: 159
  average time/residue: 0.0854
  time to fit residues: 18.6096
Evaluate side-chains
  147 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  450 PHE
Chi-restraints excluded: chain R residue  466 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 53 optimal weight:    0.4980
   chunk 40 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
B 340 ASN
N  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.144713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.126490 restraints weight = 14007.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.127040 restraints weight = 11258.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.127855 restraints weight = 9940.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.128397 restraints weight = 8112.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.128592 restraints weight = 6589.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8286  Z= 0.104
  Angle     :  0.547  10.992  11259  Z= 0.280
  Chirality :  0.039   0.128   1301
  Planarity :  0.003   0.033   1446
  Dihedral  :  4.266  31.821   1159
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 23.60 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.27), residues: 1054
  helix:  1.09 (0.26), residues: 397
  sheet: -0.67 (0.35), residues: 203
  loop : -0.52 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG N 105 
 TYR   0.009   0.001   TYR R 459 
 PHE   0.033   0.001   PHE B 199 
 TRP   0.027   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8282)
  covalent geometry    : angle       0.54626 (11251)
  SS BOND              : bond        0.00350 (    4)
  SS BOND              : angle       0.99563 (    8)
  hydrogen bonds       : bond        0.03457 (  349)
  hydrogen bonds       : angle       4.54794 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.3340 (mm110) cc_final: 0.3060 (mm110)
REVERT: A  369 CYS cc_start: 0.6602 (p) cc_final: 0.6270 (m)
REVERT: B   23 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6702 (tttp)
REVERT: B   45 MET cc_start: 0.7037 (mtp) cc_final: 0.6631 (mtp)
REVERT: B   52 ARG cc_start: 0.7325 (mmt90) cc_final: 0.6762 (mtt90)
REVERT: B  205 ASP cc_start: 0.8239 (p0) cc_final: 0.7943 (p0)
REVERT: B  219 ARG cc_start: 0.8041 (mtp-110) cc_final: 0.7786 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6216 (m-80)
REVERT: B  254 ASP cc_start: 0.6142 (t70) cc_final: 0.5912 (t70)
REVERT: B  261 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6461 (mp)
REVERT: N   83 MET cc_start: 0.7037 (mmt) cc_final: 0.6819 (mmt)
REVERT: P   15 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6349 (tt)
REVERT: R  231 MET cc_start: 0.7691 (mmp) cc_final: 0.6432 (mtt)
  outliers start: 33
  outliers final: 25
  residues processed: 150
  average time/residue: 0.0749
  time to fit residues: 15.8099
Evaluate side-chains
  152 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  450 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
B 340 ASN
N  53 GLN
N  74 ASN
P  10 ASN
R 295 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.145108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.126531 restraints weight = 14115.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127078 restraints weight = 10693.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.128030 restraints weight = 8973.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128484 restraints weight = 7409.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.128562 restraints weight = 6370.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8286  Z= 0.104
  Angle     :  0.545  10.069  11259  Z= 0.280
  Chirality :  0.039   0.128   1301
  Planarity :  0.003   0.032   1446
  Dihedral  :  4.193  31.405   1159
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 22.85 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.26), residues: 1054
  helix:  0.95 (0.26), residues: 404
  sheet: -0.64 (0.35), residues: 205
  loop : -0.51 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N 105 
 TYR   0.009   0.001   TYR R 459 
 PHE   0.029   0.001   PHE B 199 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8282)
  covalent geometry    : angle       0.54445 (11251)
  SS BOND              : bond        0.00344 (    4)
  SS BOND              : angle       0.99336 (    8)
  hydrogen bonds       : bond        0.03409 (  349)
  hydrogen bonds       : angle       4.48525 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 129
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7509 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6519 (p) cc_final: 0.6248 (m)
REVERT: B   23 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6726 (tttp)
REVERT: B   45 MET cc_start: 0.7036 (mtp) cc_final: 0.6625 (mtp)
REVERT: B   52 ARG cc_start: 0.7207 (mmt90) cc_final: 0.6756 (mtt90)
REVERT: B  205 ASP cc_start: 0.8214 (p0) cc_final: 0.7932 (p0)
REVERT: B  219 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7784 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6217 (m-80)
REVERT: B  254 ASP cc_start: 0.6102 (t70) cc_final: 0.5881 (t70)
REVERT: B  261 LEU cc_start: 0.6689 (mm) cc_final: 0.6324 (mp)
REVERT: N   83 MET cc_start: 0.7068 (mmt) cc_final: 0.6857 (mmt)
REVERT: P   15 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6434 (tt)
REVERT: R  231 MET cc_start: 0.7724 (mmp) cc_final: 0.6430 (mtt)
  outliers start: 36
  outliers final: 27
  residues processed: 153
  average time/residue: 0.0877
  time to fit residues: 18.3729
Evaluate side-chains
  149 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  392 THR
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  450 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 97 optimal weight:    0.0470
   chunk 54 optimal weight:    0.0870
   chunk 30 optimal weight:    7.9990
   chunk 80 optimal weight:   50.0000
   chunk 101 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
A  23 ASN
B 340 ASN
N  74 ASN
P  10 ASN
R 295 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.149623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.131442 restraints weight = 13898.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.131273 restraints weight = 11103.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.132409 restraints weight = 9440.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.132886 restraints weight = 7467.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133004 restraints weight = 6824.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8286  Z= 0.100
  Angle     :  0.547  10.655  11259  Z= 0.280
  Chirality :  0.038   0.131   1301
  Planarity :  0.003   0.034   1446
  Dihedral  :  4.094  31.808   1159
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.47 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.27), residues: 1054
  helix:  1.12 (0.27), residues: 395
  sheet: -0.59 (0.36), residues: 203
  loop : -0.45 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG N 105 
 TYR   0.008   0.001   TYR R 459 
 PHE   0.029   0.001   PHE B 199 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.003   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 8282)
  covalent geometry    : angle       0.54631 (11251)
  SS BOND              : bond        0.00283 (    4)
  SS BOND              : angle       0.94921 (    8)
  hydrogen bonds       : bond        0.03289 (  349)
  hydrogen bonds       : angle       4.42279 (  996)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7411 (mmm-85)
REVERT: B   23 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6736 (tttp)
REVERT: B   52 ARG cc_start: 0.7078 (mmt90) cc_final: 0.6651 (mtt90)
REVERT: B  205 ASP cc_start: 0.8183 (p0) cc_final: 0.7847 (p0)
REVERT: B  219 ARG cc_start: 0.7978 (mtp-110) cc_final: 0.7731 (ttt-90)
REVERT: B  223 THR cc_start: 0.7212 (t) cc_final: 0.6829 (p)
REVERT: B  234 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6272 (m-80)
REVERT: B  261 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6301 (mp)
REVERT: B  264 TYR cc_start: 0.8359 (m-80) cc_final: 0.8127 (m-10)
REVERT: N   34 MET cc_start: 0.8341 (mmm) cc_final: 0.8103 (mmm)
REVERT: N   83 MET cc_start: 0.7017 (mmt) cc_final: 0.6776 (mmt)
REVERT: R  231 MET cc_start: 0.7687 (mmp) cc_final: 0.6454 (mtt)
REVERT: R  237 ILE cc_start: 0.8157 (tp) cc_final: 0.7853 (tp)
  outliers start: 27
  outliers final: 21
  residues processed: 141
  average time/residue: 0.0826
  time to fit residues: 16.2266
Evaluate side-chains
  145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue  235 VAL
Chi-restraints excluded: chain R residue  310 ILE
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  423 VAL
Chi-restraints excluded: chain R residue  450 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0770
   chunk 66 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.1544

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
B 340 ASN
N  53 GLN
N  74 ASN
P  10 ASN
R 220 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.147661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.128868 restraints weight = 13885.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.128469 restraints weight = 12765.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.129594 restraints weight = 10558.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130231 restraints weight = 8293.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130416 restraints weight = 7193.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.4278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8286  Z= 0.111
  Angle     :  0.548  10.410  11259  Z= 0.281
  Chirality :  0.039   0.130   1301
  Planarity :  0.003   0.039   1446
  Dihedral  :  4.133  32.551   1159
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.47 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.26), residues: 1054
  helix:  1.03 (0.26), residues: 405
  sheet: -0.59 (0.36), residues: 201
  loop : -0.56 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG N 105 
 TYR   0.009   0.001   TYR R 459 
 PHE   0.030   0.001   PHE B 199 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8282)
  covalent geometry    : angle       0.54750 (11251)
  SS BOND              : bond        0.00411 (    4)
  SS BOND              : angle       1.07315 (    8)
  hydrogen bonds       : bond        0.03396 (  349)
  hydrogen bonds       : angle       4.43228 (  996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1270.02 seconds
wall clock time: 22 minutes 39.24 seconds (1359.24 seconds total)