Starting phenix.real_space_refine
on Fri Jul 25 19:49:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vvn_32145/07_2025/7vvn_32145.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vvn_32145/07_2025/7vvn_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vvn_32145/07_2025/7vvn_32145.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vvn_32145/07_2025/7vvn_32145.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vvn_32145/07_2025/7vvn_32145.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vvn_32145/07_2025/7vvn_32145.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2}
          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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 1}
          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: {'GLN:plan1': 2, 'ASP:plan': 1, 'PHE%COO:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 5, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 252
  Time building chain proxies: 5.29, per 1000 atoms: 0.65
  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: 2.28
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.86
  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: 2.37

  Time building geometry restraints manager: 2.34 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:             13.850
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.700
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.960
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (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
 TRP   0.032   0.007   TRP B 339 
 HIS   0.023   0.005   HIS R 420 
 PHE   0.068   0.006   PHE R 335 
 TYR   0.058   0.007   TYR B  59 
 ARG   0.015   0.002   ARG N  72 

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

*********************** 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  : 0.821 
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: 0.7584 (ptmt)
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: 0.7288 (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: 0.7734 (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: 0.7152 (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: 0.6147 (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: 0.2542
  time to fit residues: 69.0052
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  : 1.046 
-------------------------------------------------------------------------------
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 89 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.143375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.120533 restraints weight = 13609.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.122962 restraints weight = 8612.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.124380 restraints weight = 6241.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8286  Z= 0.194
  Angle     :  0.654   7.560  11259  Z= 0.347
  Chirality :  0.042   0.146   1301
  Planarity :  0.004   0.033   1446
  Dihedral  :  5.322  38.344   1163
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.36 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.25), residues: 1054
  helix:  0.46 (0.25), residues: 409
  sheet: -1.72 (0.32), residues: 215
  loop : -1.25 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.008   0.001   HIS A 347 
 PHE   0.025   0.002   PHE R 454 
 TYR   0.017   0.002   TYR B 105 
 ARG   0.005   0.001   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05175 (  349)
  hydrogen bonds       : angle       5.69517 (  996)
  SS BOND              : bond        0.00721 (    4)
  SS BOND              : angle       1.67259 (    8)
  covalent geometry    : bond        0.00437 ( 8282)
  covalent geometry    : angle       0.65298 (11251)

*********************** 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
  171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.4419 (mm-40) cc_final: 0.4171 (mm110)
REVERT: A   28 LYS cc_start: 0.6626 (tttm) cc_final: 0.6353 (ttmt)
REVERT: A  360 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7092 (tp30)
REVERT: B   23 LYS cc_start: 0.7328 (mmmt) cc_final: 0.6767 (mmtp)
REVERT: B  219 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7727 (ttp-170)
REVERT: R  231 MET cc_start: 0.7260 (mmt) cc_final: 0.6979 (mmp)
REVERT: R  413 LEU cc_start: 0.7138 (tt) cc_final: 0.6885 (tp)
REVERT: R  466 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7674 (t)
REVERT: R  470 ILE cc_start: 0.8234 (tt) cc_final: 0.7959 (pt)
  outliers start: 20
  outliers final: 14
  residues processed: 165
  average time/residue: 0.2372
  time to fit residues: 51.1202
Evaluate side-chains
  137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  233 CYS
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  365 VAL
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 49 optimal weight:    0.9980
   chunk 105 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
N  53 GLN
N  74 ASN
P  10 ASN
** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 440 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.146032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.123306 restraints weight = 13594.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.125914 restraints weight = 8500.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.127743 restraints weight = 6063.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2810

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= 0.126
  Angle     :  0.559   6.197  11259  Z= 0.298
  Chirality :  0.040   0.143   1301
  Planarity :  0.003   0.027   1446
  Dihedral  :  4.764  27.749   1159
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.48 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.26), residues: 1054
  helix:  0.89 (0.26), residues: 403
  sheet: -1.32 (0.32), residues: 212
  loop : -1.01 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.019   0.001   PHE R 454 
 TYR   0.019   0.001   TYR R 191 
 ARG   0.005   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  349)
  hydrogen bonds       : angle       5.22381 (  996)
  SS BOND              : bond        0.00468 (    4)
  SS BOND              : angle       1.25164 (    8)
  covalent geometry    : bond        0.00279 ( 8282)
  covalent geometry    : angle       0.55776 (11251)

*********************** 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
  170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.4678 (mm-40) cc_final: 0.4444 (mm110)
REVERT: A   27 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7506 (mm-30)
REVERT: A   28 LYS cc_start: 0.6550 (tttm) cc_final: 0.6282 (ttmm)
REVERT: B    6 GLN cc_start: 0.4298 (tm-30) cc_final: 0.3830 (pt0)
REVERT: B   23 LYS cc_start: 0.7308 (mmmt) cc_final: 0.6848 (mppt)
REVERT: B   82 TRP cc_start: 0.7596 (m-90) cc_final: 0.6935 (m-90)
REVERT: B  215 GLU cc_start: 0.6939 (mp0) cc_final: 0.6643 (mt-10)
REVERT: B  219 ARG cc_start: 0.8097 (mtp-110) cc_final: 0.7850 (ttt-90)
REVERT: B  261 LEU cc_start: 0.6706 (mm) cc_final: 0.6281 (mp)
REVERT: R  231 MET cc_start: 0.7361 (mmt) cc_final: 0.7122 (mmp)
REVERT: R  466 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7662 (t)
  outliers start: 23
  outliers final: 14
  residues processed: 164
  average time/residue: 0.2190
  time to fit residues: 47.9797
Evaluate side-chains
  145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
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 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 82 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 74 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    2.7964

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
N  74 ASN
P  10 ASN
R 374 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.138937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.119873 restraints weight = 14289.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.119910 restraints weight = 11870.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.120283 restraints weight = 10284.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8286  Z= 0.180
  Angle     :  0.597   7.297  11259  Z= 0.319
  Chirality :  0.042   0.149   1301
  Planarity :  0.004   0.033   1446
  Dihedral  :  4.849  26.193   1159
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 19.60 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.26), residues: 1054
  helix:  0.85 (0.26), residues: 391
  sheet: -1.38 (0.34), residues: 201
  loop : -0.83 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 347 
 PHE   0.026   0.002   PHE R 454 
 TYR   0.019   0.002   TYR B 105 
 ARG   0.005   0.001   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 (  349)
  hydrogen bonds       : angle       5.19970 (  996)
  SS BOND              : bond        0.00686 (    4)
  SS BOND              : angle       1.48141 (    8)
  covalent geometry    : bond        0.00414 ( 8282)
  covalent geometry    : angle       0.59588 (11251)

*********************** 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
  168 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6870 (tttp)
REVERT: B   52 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6876 (mtt90)
REVERT: B  215 GLU cc_start: 0.6856 (mp0) cc_final: 0.6483 (mt-10)
REVERT: B  219 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7855 (ttt-90)
REVERT: B  261 LEU cc_start: 0.6783 (mm) cc_final: 0.6423 (mp)
REVERT: B  284 LEU cc_start: 0.7339 (mp) cc_final: 0.7128 (tp)
REVERT: R  231 MET cc_start: 0.7517 (mmt) cc_final: 0.7192 (mmp)
REVERT: R  466 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7742 (t)
  outliers start: 36
  outliers final: 25
  residues processed: 161
  average time/residue: 0.2024
  time to fit residues: 44.4710
Evaluate side-chains
  142 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   54 HIS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 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 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  292 LEU
Chi-restraints excluded: chain R residue  310 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 50 optimal weight:    0.4980
   chunk 78 optimal weight:    0.0070
   chunk 64 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.8802

-------------------------------------------------------------------------------
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
P  10 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.141016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.121967 restraints weight = 13991.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.122281 restraints weight = 11624.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.122501 restraints weight = 9809.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8286  Z= 0.137
  Angle     :  0.560   7.960  11259  Z= 0.295
  Chirality :  0.040   0.144   1301
  Planarity :  0.003   0.036   1446
  Dihedral  :  4.670  26.831   1159
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 19.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.26), residues: 1054
  helix:  0.95 (0.27), residues: 393
  sheet: -1.10 (0.33), residues: 218
  loop : -0.67 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 347 
 PHE   0.028   0.002   PHE A 222 
 TYR   0.013   0.001   TYR R 459 
 ARG   0.003   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  349)
  hydrogen bonds       : angle       4.99555 (  996)
  SS BOND              : bond        0.00506 (    4)
  SS BOND              : angle       1.20765 (    8)
  covalent geometry    : bond        0.00312 ( 8282)
  covalent geometry    : angle       0.55896 (11251)

*********************** 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
  176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7701 (mmm-85)
REVERT: A  369 CYS cc_start: 0.7023 (p) cc_final: 0.6401 (m)
REVERT: B   23 LYS cc_start: 0.7225 (mmmt) cc_final: 0.6891 (tttp)
REVERT: B   52 ARG cc_start: 0.7294 (mmt90) cc_final: 0.6983 (mtt90)
REVERT: B  215 GLU cc_start: 0.6772 (mp0) cc_final: 0.6460 (mt-10)
REVERT: B  219 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7783 (ttt-90)
REVERT: R  231 MET cc_start: 0.7524 (mmt) cc_final: 0.7227 (mmp)
REVERT: R  466 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7738 (t)
  outliers start: 41
  outliers final: 29
  residues processed: 165
  average time/residue: 0.1863
  time to fit residues: 42.4100
Evaluate side-chains
  151 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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  384 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 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 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  292 LEU
Chi-restraints excluded: chain R residue  310 ILE
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  407 LEU
Chi-restraints excluded: chain R residue  466 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0040
   chunk 85 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.144086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.124940 restraints weight = 14074.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.125314 restraints weight = 11210.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.126969 restraints weight = 9353.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.3716

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= 0.108
  Angle     :  0.537   9.900  11259  Z= 0.281
  Chirality :  0.039   0.130   1301
  Planarity :  0.003   0.037   1446
  Dihedral  :  4.426  31.863   1159
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.27), residues: 1054
  helix:  0.96 (0.26), residues: 401
  sheet: -0.87 (0.35), residues: 203
  loop : -0.53 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.018   0.001   PHE R 454 
 TYR   0.011   0.001   TYR B 264 
 ARG   0.003   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  349)
  hydrogen bonds       : angle       4.72286 (  996)
  SS BOND              : bond        0.00355 (    4)
  SS BOND              : angle       0.97862 (    8)
  covalent geometry    : bond        0.00238 ( 8282)
  covalent geometry    : angle       0.53611 (11251)

*********************** 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
  175 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  369 CYS cc_start: 0.6831 (p) cc_final: 0.6242 (m)
REVERT: B   23 LYS cc_start: 0.7269 (mmmt) cc_final: 0.6904 (tttp)
REVERT: B   52 ARG cc_start: 0.7194 (mmt90) cc_final: 0.6968 (mtt90)
REVERT: B  215 GLU cc_start: 0.6882 (mp0) cc_final: 0.6675 (mt-10)
REVERT: B  219 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7717 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6391 (m-80)
REVERT: B  254 ASP cc_start: 0.6165 (t70) cc_final: 0.5921 (t70)
REVERT: B  261 LEU cc_start: 0.6759 (mm) cc_final: 0.6447 (mp)
REVERT: P   15 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6333 (tt)
REVERT: R  292 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7873 (tp)
REVERT: R  466 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7694 (t)
  outliers start: 37
  outliers final: 24
  residues processed: 161
  average time/residue: 0.1982
  time to fit residues: 43.7789
Evaluate side-chains
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
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  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  286 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 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   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  292 LEU
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
Chi-restraints excluded: chain R residue  466 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 80 optimal weight:   50.0000
   chunk 67 optimal weight:    9.9990
   chunk 94 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.137112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.118141 restraints weight = 14369.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.118682 restraints weight = 11775.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.119064 restraints weight = 9603.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   8286  Z= 0.240
  Angle     :  0.668   9.971  11259  Z= 0.349
  Chirality :  0.043   0.164   1301
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.017  32.196   1159
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 21.47 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.26), residues: 1054
  helix:  0.67 (0.26), residues: 394
  sheet: -1.19 (0.33), residues: 208
  loop : -0.72 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.009   0.002   HIS A 347 
 PHE   0.027   0.002   PHE R 454 
 TYR   0.019   0.002   TYR B 105 
 ARG   0.004   0.001   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04557 (  349)
  hydrogen bonds       : angle       5.18061 (  996)
  SS BOND              : bond        0.00819 (    4)
  SS BOND              : angle       1.70347 (    8)
  covalent geometry    : bond        0.00553 ( 8282)
  covalent geometry    : angle       0.66631 (11251)

*********************** 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
  163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 117
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7715 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6902 (p) cc_final: 0.6388 (m)
REVERT: B   23 LYS cc_start: 0.7218 (mmmt) cc_final: 0.6669 (mmtm)
REVERT: B   52 ARG cc_start: 0.7343 (mmt90) cc_final: 0.6773 (mtt90)
REVERT: B  215 GLU cc_start: 0.7007 (mp0) cc_final: 0.6703 (mt-10)
REVERT: B  219 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7700 (ttp-170)
REVERT: B  234 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.6170 (m-80)
REVERT: B  254 ASP cc_start: 0.6604 (t70) cc_final: 0.6396 (t70)
REVERT: B  261 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6442 (mp)
REVERT: B  340 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7672 (t160)
REVERT: R  192 THR cc_start: 0.7705 (m) cc_final: 0.7328 (p)
REVERT: R  327 PHE cc_start: 0.7363 (t80) cc_final: 0.7127 (t80)
REVERT: R  466 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7884 (t)
  outliers start: 46
  outliers final: 33
  residues processed: 152
  average time/residue: 0.2010
  time to fit residues: 41.4886
Evaluate side-chains
  146 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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   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  225 HIS
Chi-restraints excluded: chain B residue  228 ASP
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  286 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 B residue  340 ASN
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   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  292 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  407 LEU
Chi-restraints excluded: chain R residue  444 GLU
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 14 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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
R 295 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.142074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.123238 restraints weight = 14177.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123524 restraints weight = 11669.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124494 restraints weight = 9349.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8286  Z= 0.117
  Angle     :  0.568   9.258  11259  Z= 0.294
  Chirality :  0.041   0.321   1301
  Planarity :  0.003   0.030   1446
  Dihedral  :  4.682  38.355   1159
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 22.85 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.26), residues: 1054
  helix:  0.86 (0.26), residues: 396
  sheet: -0.91 (0.34), residues: 204
  loop : -0.58 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.018   0.001   PHE A 222 
 TYR   0.013   0.001   TYR B 264 
 ARG   0.003   0.000   ARG A 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  349)
  hydrogen bonds       : angle       4.81681 (  996)
  SS BOND              : bond        0.00414 (    4)
  SS BOND              : angle       1.04662 (    8)
  covalent geometry    : bond        0.00255 ( 8282)
  covalent geometry    : angle       0.56764 (11251)

*********************** 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: 35
    poor density    : 125
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: A   38 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7638 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6643 (p) cc_final: 0.6327 (m)
REVERT: B   23 LYS cc_start: 0.7184 (mmmt) cc_final: 0.6817 (tttp)
REVERT: B   45 MET cc_start: 0.6978 (mtp) cc_final: 0.6584 (mtp)
REVERT: B  215 GLU cc_start: 0.7064 (mp0) cc_final: 0.6779 (mt-10)
REVERT: B  219 ARG cc_start: 0.8191 (mtp-110) cc_final: 0.7791 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6271 (m-80)
REVERT: B  254 ASP cc_start: 0.6358 (t70) cc_final: 0.6102 (t70)
REVERT: B  261 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6297 (mp)
REVERT: B  317 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7521 (p)
REVERT: P   15 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6402 (tt)
REVERT: R  192 THR cc_start: 0.7606 (m) cc_final: 0.7262 (p)
REVERT: R  292 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.7984 (tp)
REVERT: R  327 PHE cc_start: 0.7311 (t80) cc_final: 0.7082 (t80)
  outliers start: 35
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1936
  time to fit residues: 39.5545
Evaluate side-chains
  147 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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  279 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain B residue   54 HIS
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  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  317 CYS
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 N residue   99 CYS
Chi-restraints excluded: chain P residue   15 LEU
Chi-restraints excluded: chain R residue  292 LEU
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  407 LEU
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 85 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 80 optimal weight:   50.0000
   chunk 97 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
G  18 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 = 0.3925 r_free = 0.3925 target = 0.144729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.124699 restraints weight = 14170.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.126624 restraints weight = 9650.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127715 restraints weight = 7386.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.4147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8286  Z= 0.121
  Angle     :  0.577   9.157  11259  Z= 0.296
  Chirality :  0.040   0.228   1301
  Planarity :  0.003   0.029   1446
  Dihedral  :  4.550  35.210   1159
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 22.97 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1054
  helix:  0.97 (0.26), residues: 394
  sheet: -0.91 (0.34), residues: 206
  loop : -0.55 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.018   0.001   PHE R 454 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.004   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  349)
  hydrogen bonds       : angle       4.70696 (  996)
  SS BOND              : bond        0.00437 (    4)
  SS BOND              : angle       1.12888 (    8)
  covalent geometry    : bond        0.00272 ( 8282)
  covalent geometry    : angle       0.57644 (11251)

*********************** 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
  153 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8116 (tpp80) cc_final: 0.7640 (mmm-85)
REVERT: A  213 GLN cc_start: 0.3559 (mm110) cc_final: 0.3245 (mm110)
REVERT: A  369 CYS cc_start: 0.6583 (p) cc_final: 0.6309 (m)
REVERT: B   23 LYS cc_start: 0.7143 (mmmt) cc_final: 0.6780 (tttp)
REVERT: B   45 MET cc_start: 0.6889 (mtp) cc_final: 0.6505 (mtp)
REVERT: B  215 GLU cc_start: 0.6839 (mp0) cc_final: 0.6603 (mt-10)
REVERT: B  219 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7738 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6259 (m-80)
REVERT: B  254 ASP cc_start: 0.6324 (t70) cc_final: 0.6067 (t70)
REVERT: B  261 LEU cc_start: 0.6678 (mm) cc_final: 0.6244 (mp)
REVERT: B  317 CYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7541 (p)
REVERT: P   15 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6431 (tt)
REVERT: R  192 THR cc_start: 0.7562 (m) cc_final: 0.7250 (p)
REVERT: R  231 MET cc_start: 0.7934 (mmp) cc_final: 0.6540 (mtt)
REVERT: R  292 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7920 (tp)
REVERT: R  327 PHE cc_start: 0.7312 (t80) cc_final: 0.7058 (t80)
  outliers start: 34
  outliers final: 28
  residues processed: 143
  average time/residue: 0.2050
  time to fit residues: 40.2923
Evaluate side-chains
  147 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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  279 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain B residue   54 HIS
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  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  317 CYS
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 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  292 LEU
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  407 LEU
Chi-restraints excluded: chain R residue  450 PHE
Chi-restraints excluded: chain R residue  474 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0270
   chunk 72 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0010
   chunk 105 optimal weight:   10.0000
   overall best weight:    1.6048

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.144497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.124422 restraints weight = 14010.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.126064 restraints weight = 9631.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127575 restraints weight = 7541.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8286  Z= 0.129
  Angle     :  0.585   9.547  11259  Z= 0.300
  Chirality :  0.040   0.171   1301
  Planarity :  0.003   0.029   1446
  Dihedral  :  4.518  32.395   1159
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 23.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1054
  helix:  0.98 (0.26), residues: 394
  sheet: -0.81 (0.34), residues: 204
  loop : -0.57 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.019   0.001   PHE R 454 
 TYR   0.012   0.001   TYR N  80 
 ARG   0.007   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  349)
  hydrogen bonds       : angle       4.70341 (  996)
  SS BOND              : bond        0.00455 (    4)
  SS BOND              : angle       1.16529 (    8)
  covalent geometry    : bond        0.00294 ( 8282)
  covalent geometry    : angle       0.58421 (11251)

********************** 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
  148 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7646 (mmm-85)
REVERT: A  369 CYS cc_start: 0.6569 (p) cc_final: 0.6320 (m)
REVERT: B   23 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6779 (tttp)
REVERT: B  215 GLU cc_start: 0.6826 (mp0) cc_final: 0.6623 (mt-10)
REVERT: B  219 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7847 (ttt-90)
REVERT: B  234 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6246 (m-80)
REVERT: B  254 ASP cc_start: 0.6367 (t70) cc_final: 0.6086 (t70)
REVERT: B  261 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6232 (mp)
REVERT: B  317 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7556 (p)
REVERT: P   15 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6443 (tt)
REVERT: R  192 THR cc_start: 0.7564 (m) cc_final: 0.7253 (p)
REVERT: R  231 MET cc_start: 0.8080 (mmp) cc_final: 0.6865 (mtt)
REVERT: R  292 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.7935 (tp)
REVERT: R  307 HIS cc_start: 0.6934 (t-90) cc_final: 0.6710 (t-90)
REVERT: R  327 PHE cc_start: 0.7322 (t80) cc_final: 0.7061 (t80)
  outliers start: 32
  outliers final: 26
  residues processed: 137
  average time/residue: 0.1912
  time to fit residues: 36.5850
Evaluate side-chains
  143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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  279 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain B residue   54 HIS
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  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  317 CYS
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 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  292 LEU
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  407 LEU
Chi-restraints excluded: chain R residue  450 PHE
Chi-restraints excluded: chain R residue  474 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 98 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0980
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.142020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.122494 restraints weight = 14259.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.123143 restraints weight = 11463.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.124357 restraints weight = 9506.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8286  Z= 0.176
  Angle     :  0.634  11.558  11259  Z= 0.326
  Chirality :  0.042   0.205   1301
  Planarity :  0.003   0.030   1446
  Dihedral  :  4.785  33.087   1159
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 23.22 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.26), residues: 1054
  helix:  0.90 (0.26), residues: 393
  sheet: -0.90 (0.33), residues: 204
  loop : -0.69 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.023   0.002   PHE R 454 
 TYR   0.014   0.002   TYR R 459 
 ARG   0.008   0.001   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  349)
  hydrogen bonds       : angle       4.90068 (  996)
  SS BOND              : bond        0.00642 (    4)
  SS BOND              : angle       1.43727 (    8)
  covalent geometry    : bond        0.00406 ( 8282)
  covalent geometry    : angle       0.63285 (11251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2629.85 seconds
wall clock time: 46 minutes 36.38 seconds (2796.38 seconds total)