Starting phenix.real_space_refine
on Thu Mar 13 13:01:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eq1_31254/03_2025/7eq1_31254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eq1_31254/03_2025/7eq1_31254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eq1_31254/03_2025/7eq1_31254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eq1_31254/03_2025/7eq1_31254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eq1_31254/03_2025/7eq1_31254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eq1_31254/03_2025/7eq1_31254.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   0.029
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      56      5.16       5
     C    5728      2.51       5
     N    1546      2.21       5
     O    1669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8999
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1959
          Classifications: {'peptide': 237}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 2212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2212
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "S"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1787
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "B"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2596
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 5.18, per 1000 atoms: 0.58
  Number of scatterers: 8999
  At special positions: 0
  Unit cell: (115.56, 117.72, 105.84, 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      56     16.00
     O    1669      8.00
     N    1546      7.00
     C    5728      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 314 " - pdb=" SG  CYS R 404 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.12
  Conformation dependent library (CDL) restraints added in 978.0 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      35.0% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 40
      removed outlier: 3.574A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.543A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.654A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.673A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.200A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.996A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.642A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 389
      removed outlier: 3.935A  pdb=" N   ILE A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 392
      No H-bonds generated for 'chain 'A' and resid 390 through 392'
    Processing helix  chain 'R' and resid 228 through 233
      removed outlier: 3.625A  pdb=" N   VAL R 231 " --> pdb=" O   TYR R 228 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 273
      removed outlier: 3.645A  pdb=" N   CYS R 256 " --> pdb=" O   SER R 252 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU R 264 " --> pdb=" O   ILE R 260 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE R 271 " --> pdb=" O   VAL R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 299
      removed outlier: 3.722A  pdb=" N   LEU R 299 " --> pdb=" O   ASN R 295 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 304
      removed outlier: 4.104A  pdb=" N   ALA R 303 " --> pdb=" O   LEU R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 344
      removed outlier: 4.228A  pdb=" N   ALA R 316 " --> pdb=" O   SER R 312 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LEU R 317 " --> pdb=" O   ALA R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 353 through 364
      removed outlier: 3.570A  pdb=" N   LEU R 361 " --> pdb=" O   LYS R 357 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 370 through 376
      removed outlier: 4.107A  pdb=" N   SER R 375 " --> pdb=" O   LEU R 371 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL R 376 " --> pdb=" O   LEU R 372 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 442
      removed outlier: 3.581A  pdb=" N   LEU R 425 " --> pdb=" O   GLY R 421 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE R 426 " --> pdb=" O   LEU R 422 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 456 through 467
    Processing helix  chain 'R' and resid 468 through 473
      removed outlier: 3.539A  pdb=" N   ALA R 473 " --> pdb=" O   TRP R 470 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 480 through 493
      removed outlier: 3.640A  pdb=" N   GLN R 484 " --> pdb=" O   PHE R 480 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   PHE R 488 " --> pdb=" O   GLN R 484 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR R 489 " --> pdb=" O   LEU R 485 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 494 through 520
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.612A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.505A  pdb=" N   ASP S 223 " --> pdb=" O   GLU S 220 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 220 through 224'
    Processing helix  chain 'Y' and resid 7 through 24
      removed outlier: 3.687A  pdb=" N   GLN Y  11 " --> pdb=" O   ALA Y   7 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LYS Y  14 " --> pdb=" O   ALA Y  10 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU Y  15 " --> pdb=" O   GLN Y  11 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL Y  16 " --> pdb=" O   ALA Y  12 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU Y  17 " --> pdb=" O   ARG Y  13 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.820A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.900A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.900A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.869A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AA6, first strand: chain 'S' and resid 147 through 148
      removed outlier: 3.738A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.720A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.696A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.065A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.582A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.928A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.221A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.716A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    417 hydrogen bonds defined for protein.
    1167 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: 2.57

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2917
        1.34 -     1.46: 2146
        1.46 -     1.58: 4053
        1.58 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 9197
  Sorted by residual:
  bond pdb=" CB  MET S 230 "
       pdb=" CG  MET S 230 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.31e-01
  bond pdb=" CG  MET B  61 "
       pdb=" SD  MET B  61 "
    ideal  model  delta    sigma   weight residual
    1.803  1.782  0.021 2.50e-02 1.60e+03 6.85e-01
  bond pdb=" CB  PRO S 236 "
       pdb=" CG  PRO S 236 "
    ideal  model  delta    sigma   weight residual
    1.506  1.475  0.031 3.90e-02 6.57e+02 6.50e-01
  bond pdb=" CB  ILE S  58 "
       pdb=" CG2 ILE S  58 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.25e-01
  bond pdb=" CB  ARG S  98 "
       pdb=" CG  ARG S  98 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.24e-01
  ... (remaining 9192 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 12200
        1.68 -     3.35: 227
        3.35 -     5.03: 39
        5.03 -     6.71: 8
        6.71 -     8.38: 1
  Bond angle restraints: 12475
  Sorted by residual:
  angle pdb=" C   ARG S 191 "
        pdb=" N   MET S 192 "
        pdb=" CA  MET S 192 "
      ideal   model   delta    sigma   weight residual
     121.54  129.92   -8.38 1.91e+00 2.74e-01 1.93e+01
  angle pdb=" CA  CYS R 404 "
        pdb=" CB  CYS R 404 "
        pdb=" SG  CYS R 404 "
      ideal   model   delta    sigma   weight residual
     114.40  120.30   -5.90 2.30e+00 1.89e-01 6.58e+00
  angle pdb=" C   VAL A 367 "
        pdb=" N   ASP A 368 "
        pdb=" CA  ASP A 368 "
      ideal   model   delta    sigma   weight residual
     121.54  126.39   -4.85 1.91e+00 2.74e-01 6.45e+00
  angle pdb=" C   PRO R 241 "
        pdb=" N   ALA R 242 "
        pdb=" CA  ALA R 242 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.98e+00
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     121.54  126.02   -4.48 1.91e+00 2.74e-01 5.49e+00
  ... (remaining 12470 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4922
       17.97 -    35.94: 420
       35.94 -    53.91: 71
       53.91 -    71.88: 10
       71.88 -    89.84: 9
  Dihedral angle restraints: 5432
    sinusoidal: 2100
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" CB  CYS R 314 "
           pdb=" SG  CYS R 314 "
           pdb=" SG  CYS R 404 "
           pdb=" CB  CYS R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.88   72.88     1      1.00e+01 1.00e-02 6.77e+01
  dihedral pdb=" CA  LEU R 235 "
           pdb=" C   LEU R 235 "
           pdb=" N   SER R 236 "
           pdb=" CA  SER R 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  VAL B 213 "
           pdb=" C   VAL B 213 "
           pdb=" N   ARG B 214 "
           pdb=" CA  ARG B 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 5429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 831
       0.031 -    0.062: 391
       0.062 -    0.093: 125
       0.093 -    0.124: 54
       0.124 -    0.155: 10
  Chirality restraints: 1411
  Sorted by residual:
  chirality pdb=" CB  ILE R 386 "
            pdb=" CA  ILE R 386 "
            pdb=" CG1 ILE R 386 "
            pdb=" CG2 ILE R 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CB  THR S  91 "
            pdb=" CA  THR S  91 "
            pdb=" OG1 THR S  91 "
            pdb=" CG2 THR S  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CA  VAL R 240 "
            pdb=" N   VAL R 240 "
            pdb=" C   VAL R 240 "
            pdb=" CB  VAL R 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 1408 not shown)

  Planarity restraints: 1581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.015 2.00e-02 2.50e+03   1.22e-02 2.97e+00
        pdb=" CG  TYR B  59 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE S 239 "    0.012 2.00e-02 2.50e+03   1.25e-02 2.75e+00
        pdb=" CG  PHE S 239 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE S 239 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE S 239 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE S 239 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE S 239 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE S 239 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 309 "   -0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO R 310 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO R 310 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 310 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1578 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 156
        2.67 -     3.23: 8576
        3.23 -     3.78: 14129
        3.78 -     4.34: 19172
        4.34 -     4.90: 31434
  Nonbonded interactions: 73467
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OD2 ASP Y  48 "
            pdb=" OG  SER B 281 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   PHE A 376 "
            pdb=" OH  TYR R 347 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.202 3.040
  ... (remaining 73462 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  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:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.600
  Find NCS groups from input model:        0.080
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
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      :  0.003   0.037   9197  Z= 0.210
  Angle     :  0.584   8.383  12475  Z= 0.310
  Chirality :  0.042   0.155   1411
  Planarity :  0.004   0.040   1581
  Dihedral  : 13.831  89.845   3278
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.59 (0.26), residues: 1134
  helix:  0.75 (0.29), residues: 363
  sheet: -0.43 (0.30), residues: 282
  loop : -1.18 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.028   0.002   PHE S 239 
 TYR   0.030   0.002   TYR B  59 
 ARG   0.006   0.000   ARG A 283 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7432 (m-30) cc_final: 0.7182 (m-30)
REVERT: A  207 ILE cc_start: 0.8337 (mm) cc_final: 0.8119 (mm)
REVERT: A  327 GLU cc_start: 0.7680 (mp0) cc_final: 0.7364 (mp0)
REVERT: R  361 LEU cc_start: 0.8508 (tp) cc_final: 0.8182 (tp)
REVERT: R  485 LEU cc_start: 0.7710 (mt) cc_final: 0.7486 (mm)
REVERT: R  492 ASN cc_start: 0.8280 (m-40) cc_final: 0.7836 (m-40)
REVERT: S  192 MET cc_start: 0.7267 (ptt) cc_final: 0.7067 (ptt)
REVERT: B   27 ASP cc_start: 0.7392 (p0) cc_final: 0.7073 (p0)
REVERT: B   37 ILE cc_start: 0.8616 (mm) cc_final: 0.8406 (mm)
REVERT: B   44 GLN cc_start: 0.6858 (mp-120) cc_final: 0.5873 (mp-120)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2477
  time to fit residues: 64.0873
Evaluate side-chains
  184 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
R 454 HIS
B  88 ASN
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.113525 restraints weight = 12727.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.96
r_work: 0.3277 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9197  Z= 0.213
  Angle     :  0.578   7.085  12475  Z= 0.303
  Chirality :  0.043   0.175   1411
  Planarity :  0.004   0.041   1581
  Dihedral  :  4.586  20.888   1251
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.92 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.50 (0.26), residues: 1134
  helix:  0.76 (0.29), residues: 374
  sheet: -0.20 (0.30), residues: 284
  loop : -1.24 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.026   0.002   PHE S  68 
 TYR   0.015   0.001   TYR A 391 
 ARG   0.008   0.001   ARG B  42 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 203
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6949 (mt-10)
REVERT: A  207 ILE cc_start: 0.8515 (mm) cc_final: 0.8192 (mm)
REVERT: A  216 LYS cc_start: 0.8488 (mppt) cc_final: 0.8041 (mppt)
REVERT: A  293 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7779 (mtmm)
REVERT: A  327 GLU cc_start: 0.7962 (mp0) cc_final: 0.7559 (mp0)
REVERT: A  356 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7240 (mtp180)
REVERT: A  374 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7813 (mtt-85)
REVERT: R  492 ASN cc_start: 0.8456 (m-40) cc_final: 0.7962 (m-40)
REVERT: S   20 LEU cc_start: 0.7998 (mp) cc_final: 0.7783 (mp)
REVERT: S  174 LEU cc_start: 0.8546 (tp) cc_final: 0.8283 (tp)
REVERT: S  202 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7859 (mtm110)
REVERT: S  223 ASP cc_start: 0.7975 (m-30) cc_final: 0.7677 (m-30)
REVERT: B   42 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.7015 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7395 (mp-120) cc_final: 0.7032 (mp-120)
REVERT: B   61 MET cc_start: 0.8122 (ptm) cc_final: 0.7889 (ptm)
REVERT: B   68 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.8090 (ttt180)
REVERT: B  246 ASP cc_start: 0.7836 (m-30) cc_final: 0.7459 (m-30)
REVERT: B  258 ASP cc_start: 0.8088 (t70) cc_final: 0.7856 (t70)
REVERT: B  275 SER cc_start: 0.7974 (t) cc_final: 0.7759 (t)
REVERT: B  315 VAL cc_start: 0.7252 (t) cc_final: 0.6951 (t)
  outliers start: 16
  outliers final: 11
  residues processed: 208
  average time/residue: 0.2538
  time to fit residues: 69.6004
Evaluate side-chains
  209 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 197
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  464 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 230 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.130197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.111632 restraints weight = 12878.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.92
r_work: 0.3262 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9197  Z= 0.236
  Angle     :  0.567   7.091  12475  Z= 0.297
  Chirality :  0.043   0.157   1411
  Planarity :  0.004   0.042   1581
  Dihedral  :  4.559  20.388   1251
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.13 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.32 (0.26), residues: 1134
  helix:  0.98 (0.28), residues: 366
  sheet: -0.12 (0.30), residues: 281
  loop : -1.15 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.020   0.002   PHE S  68 
 TYR   0.017   0.001   TYR A 391 
 ARG   0.004   0.000   ARG B  96 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 201
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7032 (mt-10)
REVERT: A  216 LYS cc_start: 0.8494 (mppt) cc_final: 0.8094 (mppt)
REVERT: A  283 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7893 (ttp80)
REVERT: A  293 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7842 (mtmm)
REVERT: A  327 GLU cc_start: 0.7926 (mp0) cc_final: 0.7512 (mp0)
REVERT: A  374 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7938 (mtt-85)
REVERT: R  492 ASN cc_start: 0.8500 (m-40) cc_final: 0.8017 (m-40)
REVERT: S  174 LEU cc_start: 0.8595 (tp) cc_final: 0.8374 (tp)
REVERT: S  202 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7868 (mtm110)
REVERT: S  223 ASP cc_start: 0.7923 (m-30) cc_final: 0.7588 (m-30)
REVERT: B   68 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.8014 (ttt180)
REVERT: B  223 THR cc_start: 0.7767 (t) cc_final: 0.7506 (p)
REVERT: B  234 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8434 (m-80)
REVERT: B  258 ASP cc_start: 0.8100 (t70) cc_final: 0.7894 (t70)
REVERT: B  275 SER cc_start: 0.7896 (t) cc_final: 0.7683 (t)
REVERT: B  317 CYS cc_start: 0.7548 (p) cc_final: 0.7295 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 208
  average time/residue: 0.2580
  time to fit residues: 71.2636
Evaluate side-chains
  213 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  464 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain S residue  193 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0970
   chunk 55 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113138 restraints weight = 12824.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.98
r_work: 0.3263 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9197  Z= 0.197
  Angle     :  0.553   7.487  12475  Z= 0.286
  Chirality :  0.042   0.171   1411
  Planarity :  0.004   0.044   1581
  Dihedral  :  4.460  20.186   1251
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.08 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.22 (0.26), residues: 1134
  helix:  1.23 (0.28), residues: 357
  sheet: -0.13 (0.30), residues: 281
  loop : -1.14 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.022   0.001   PHE S  68 
 TYR   0.015   0.001   TYR A 391 
 ARG   0.003   0.000   ARG B  96 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7005 (mt-10)
REVERT: A  216 LYS cc_start: 0.8498 (mppt) cc_final: 0.8068 (mppt)
REVERT: A  293 LYS cc_start: 0.8216 (mtmt) cc_final: 0.8012 (mtpp)
REVERT: A  327 GLU cc_start: 0.7963 (mp0) cc_final: 0.7529 (mp0)
REVERT: A  345 PHE cc_start: 0.7845 (m-80) cc_final: 0.7381 (m-80)
REVERT: A  374 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7975 (mtt-85)
REVERT: R  492 ASN cc_start: 0.8450 (m-40) cc_final: 0.7998 (m-40)
REVERT: S  174 LEU cc_start: 0.8530 (tp) cc_final: 0.8286 (tp)
REVERT: S  202 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7802 (mtm110)
REVERT: S  223 ASP cc_start: 0.8020 (m-30) cc_final: 0.7665 (m-30)
REVERT: B   22 ARG cc_start: 0.7226 (mtt90) cc_final: 0.7012 (mtt90)
REVERT: B   42 ARG cc_start: 0.7487 (ttt-90) cc_final: 0.7012 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7549 (mp-120) cc_final: 0.6768 (mp10)
REVERT: B   68 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.8063 (ttt180)
REVERT: B  219 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7478 (mpt180)
REVERT: B  223 THR cc_start: 0.7781 (t) cc_final: 0.7513 (p)
REVERT: B  234 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8444 (m-80)
REVERT: B  275 SER cc_start: 0.7978 (t) cc_final: 0.7730 (t)
REVERT: B  283 ARG cc_start: 0.8449 (tpt170) cc_final: 0.7996 (tpt170)
  outliers start: 25
  outliers final: 15
  residues processed: 214
  average time/residue: 0.2738
  time to fit residues: 77.5293
Evaluate side-chains
  215 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 199
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain S residue   93 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.129765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.111204 restraints weight = 12776.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.91
r_work: 0.3253 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9197  Z= 0.250
  Angle     :  0.573   6.417  12475  Z= 0.297
  Chirality :  0.043   0.174   1411
  Planarity :  0.004   0.044   1581
  Dihedral  :  4.573  20.277   1251
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.13 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.32 (0.26), residues: 1134
  helix:  1.06 (0.28), residues: 366
  sheet: -0.27 (0.30), residues: 282
  loop : -1.12 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.031   0.002   PHE S  68 
 TYR   0.017   0.001   TYR A 391 
 ARG   0.003   0.000   ARG B  42 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: A  327 GLU cc_start: 0.7956 (mp0) cc_final: 0.7494 (mp0)
REVERT: A  374 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.8115 (mtt-85)
REVERT: R  492 ASN cc_start: 0.8501 (m-40) cc_final: 0.8021 (m-40)
REVERT: S  174 LEU cc_start: 0.8701 (tp) cc_final: 0.8468 (tp)
REVERT: S  202 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7828 (mtm110)
REVERT: S  223 ASP cc_start: 0.7960 (m-30) cc_final: 0.7540 (m-30)
REVERT: S  227 TYR cc_start: 0.8432 (m-80) cc_final: 0.8143 (m-80)
REVERT: B   42 ARG cc_start: 0.7481 (ttt-90) cc_final: 0.7021 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6753 (mp10)
REVERT: B   59 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7471 (m-10)
REVERT: B  219 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7501 (mmt180)
REVERT: B  223 THR cc_start: 0.7831 (t) cc_final: 0.7577 (p)
REVERT: B  234 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8440 (m-80)
REVERT: B  275 SER cc_start: 0.7932 (t) cc_final: 0.7698 (t)
  outliers start: 25
  outliers final: 18
  residues processed: 214
  average time/residue: 0.3596
  time to fit residues: 101.5894
Evaluate side-chains
  219 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 198
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  370 VAL
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain R residue  508 CYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 78 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111145 restraints weight = 12706.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.89
r_work: 0.3251 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9197  Z= 0.271
  Angle     :  0.579   7.226  12475  Z= 0.300
  Chirality :  0.043   0.188   1411
  Planarity :  0.004   0.044   1581
  Dihedral  :  4.631  20.735   1251
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.13 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.39 (0.26), residues: 1134
  helix:  1.01 (0.28), residues: 362
  sheet: -0.42 (0.31), residues: 272
  loop : -1.05 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.029   0.002   PHE S  68 
 TYR   0.019   0.002   TYR A 391 
 ARG   0.003   0.000   ARG B  68 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 204
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: A  216 LYS cc_start: 0.8459 (mppt) cc_final: 0.8191 (mppt)
REVERT: A  293 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7734 (mtmm)
REVERT: A  327 GLU cc_start: 0.7934 (mp0) cc_final: 0.7450 (mp0)
REVERT: A  374 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.8094 (mtt180)
REVERT: A  392 GLU cc_start: 0.6734 (pt0) cc_final: 0.6492 (pt0)
REVERT: R  492 ASN cc_start: 0.8494 (m-40) cc_final: 0.7998 (m-40)
REVERT: S  174 LEU cc_start: 0.8711 (tp) cc_final: 0.8460 (tp)
REVERT: S  202 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7864 (mtm110)
REVERT: S  223 ASP cc_start: 0.7924 (m-30) cc_final: 0.7491 (m-30)
REVERT: S  227 TYR cc_start: 0.8441 (m-80) cc_final: 0.8145 (m-80)
REVERT: B   42 ARG cc_start: 0.7402 (ttt-90) cc_final: 0.6971 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6748 (mp10)
REVERT: B   59 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7574 (m-10)
REVERT: B   68 ARG cc_start: 0.8273 (ttt-90) cc_final: 0.8070 (ttt180)
REVERT: B  219 ARG cc_start: 0.7874 (mmt180) cc_final: 0.7475 (mmt180)
REVERT: B  223 THR cc_start: 0.7827 (t) cc_final: 0.7589 (p)
REVERT: B  234 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8441 (m-80)
REVERT: B  275 SER cc_start: 0.7949 (t) cc_final: 0.7718 (t)
  outliers start: 33
  outliers final: 25
  residues processed: 219
  average time/residue: 0.2683
  time to fit residues: 77.5449
Evaluate side-chains
  230 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  370 VAL
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  423 THR
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  464 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain R residue  508 CYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 100 optimal weight:    0.2980
   chunk 77 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.131529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112975 restraints weight = 12889.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.92
r_work: 0.3274 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9197  Z= 0.195
  Angle     :  0.558   7.657  12475  Z= 0.286
  Chirality :  0.042   0.194   1411
  Planarity :  0.004   0.044   1581
  Dihedral  :  4.462  20.242   1251
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.85 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: 1134
  helix:  1.27 (0.29), residues: 353
  sheet: -0.43 (0.30), residues: 273
  loop : -1.03 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.022   0.001   PHE S  68 
 TYR   0.015   0.001   TYR A 391 
 ARG   0.005   0.000   ARG A 283 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 208
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7006 (mt-10)
REVERT: A  216 LYS cc_start: 0.8428 (mppt) cc_final: 0.8055 (mppt)
REVERT: A  231 ARG cc_start: 0.8151 (ptp90) cc_final: 0.7927 (ptp90)
REVERT: A  292 ASN cc_start: 0.8357 (t0) cc_final: 0.7995 (t0)
REVERT: A  294 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6717 (mm-40)
REVERT: A  327 GLU cc_start: 0.7913 (mp0) cc_final: 0.7434 (mp0)
REVERT: A  374 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.8077 (mtt180)
REVERT: R  492 ASN cc_start: 0.8466 (m-40) cc_final: 0.8013 (m-40)
REVERT: S   32 PHE cc_start: 0.8249 (m-80) cc_final: 0.7967 (m-80)
REVERT: S   68 PHE cc_start: 0.7771 (m-80) cc_final: 0.7418 (m-10)
REVERT: S  174 LEU cc_start: 0.8590 (tp) cc_final: 0.8355 (tp)
REVERT: S  202 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7824 (mtm110)
REVERT: S  223 ASP cc_start: 0.7906 (m-30) cc_final: 0.7485 (m-30)
REVERT: S  227 TYR cc_start: 0.8424 (m-80) cc_final: 0.8082 (m-80)
REVERT: B   42 ARG cc_start: 0.7392 (ttt-90) cc_final: 0.6923 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6640 (mp10)
REVERT: B   55 LEU cc_start: 0.8275 (mp) cc_final: 0.8032 (mp)
REVERT: B   59 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7443 (m-10)
REVERT: B  210 LEU cc_start: 0.8460 (tp) cc_final: 0.8035 (tp)
REVERT: B  219 ARG cc_start: 0.7872 (mmt180) cc_final: 0.7494 (mpt180)
REVERT: B  223 THR cc_start: 0.7797 (t) cc_final: 0.7541 (p)
REVERT: B  234 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8441 (m-80)
REVERT: B  275 SER cc_start: 0.7948 (t) cc_final: 0.7703 (t)
  outliers start: 33
  outliers final: 23
  residues processed: 225
  average time/residue: 0.2449
  time to fit residues: 72.6951
Evaluate side-chains
  233 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  370 VAL
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  423 THR
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain R residue  508 CYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    0.0070
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.3404

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.111154 restraints weight = 12982.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.90
r_work: 0.3242 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9197  Z= 0.322
  Angle     :  0.611   8.075  12475  Z= 0.316
  Chirality :  0.044   0.206   1411
  Planarity :  0.004   0.043   1581
  Dihedral  :  4.706  21.228   1251
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.26 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.44 (0.25), residues: 1134
  helix:  0.97 (0.28), residues: 364
  sheet: -0.37 (0.30), residues: 292
  loop : -1.17 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.033   0.002   PHE S  68 
 TYR   0.021   0.002   TYR A 391 
 ARG   0.004   0.000   ARG B  52 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 205
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  216 LYS cc_start: 0.8451 (mppt) cc_final: 0.8192 (mppt)
REVERT: A  231 ARG cc_start: 0.8174 (ptp90) cc_final: 0.7952 (ptp90)
REVERT: A  294 GLN cc_start: 0.7012 (mm-40) cc_final: 0.6809 (mm-40)
REVERT: A  374 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.8197 (mtt180)
REVERT: R  492 ASN cc_start: 0.8490 (m-40) cc_final: 0.7970 (m-40)
REVERT: S   32 PHE cc_start: 0.8287 (m-80) cc_final: 0.7771 (m-80)
REVERT: S  174 LEU cc_start: 0.8685 (tp) cc_final: 0.8415 (tp)
REVERT: S  202 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7833 (mtm110)
REVERT: S  223 ASP cc_start: 0.7922 (m-30) cc_final: 0.7496 (m-30)
REVERT: S  224 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.8022 (t)
REVERT: B   42 ARG cc_start: 0.7506 (ttt-90) cc_final: 0.7056 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6674 (mp10)
REVERT: B   59 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7689 (m-10)
REVERT: B  219 ARG cc_start: 0.7944 (mmt180) cc_final: 0.7591 (mmp80)
REVERT: B  223 THR cc_start: 0.7954 (t) cc_final: 0.7720 (p)
REVERT: B  234 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (m-80)
REVERT: B  275 SER cc_start: 0.7989 (t) cc_final: 0.7771 (t)
  outliers start: 36
  outliers final: 27
  residues processed: 223
  average time/residue: 0.2457
  time to fit residues: 72.7143
Evaluate side-chains
  233 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  370 VAL
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  423 THR
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain R residue  508 CYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  224 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 77 optimal weight:    0.9980
   chunk 109 optimal weight:    4.9990
   chunk 105 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0270
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.114396 restraints weight = 12772.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.91
r_work: 0.3282 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9197  Z= 0.180
  Angle     :  0.564   7.799  12475  Z= 0.290
  Chirality :  0.042   0.188   1411
  Planarity :  0.004   0.042   1581
  Dihedral  :  4.460  20.274   1251
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.28 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.24 (0.26), residues: 1134
  helix:  1.30 (0.29), residues: 353
  sheet: -0.34 (0.30), residues: 283
  loop : -1.07 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE S  68 
 TYR   0.013   0.001   TYR A 391 
 ARG   0.004   0.000   ARG A 283 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7006 (mt-10)
REVERT: A  216 LYS cc_start: 0.8449 (mppt) cc_final: 0.8140 (mppt)
REVERT: A  246 PHE cc_start: 0.8247 (t80) cc_final: 0.8011 (t80)
REVERT: A  292 ASN cc_start: 0.8358 (t0) cc_final: 0.7995 (t0)
REVERT: A  294 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6809 (mm-40)
REVERT: A  327 GLU cc_start: 0.7929 (mp0) cc_final: 0.7414 (mp0)
REVERT: A  374 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8093 (mtt180)
REVERT: R  492 ASN cc_start: 0.8425 (m-40) cc_final: 0.7995 (m-40)
REVERT: S   32 PHE cc_start: 0.8267 (m-80) cc_final: 0.8056 (m-80)
REVERT: S  174 LEU cc_start: 0.8593 (tp) cc_final: 0.8379 (tp)
REVERT: S  202 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7816 (mtm110)
REVERT: S  223 ASP cc_start: 0.7872 (m-30) cc_final: 0.7522 (m-30)
REVERT: S  224 VAL cc_start: 0.8205 (p) cc_final: 0.7983 (t)
REVERT: B   42 ARG cc_start: 0.7409 (ttt-90) cc_final: 0.6955 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6584 (mp10)
REVERT: B   55 LEU cc_start: 0.8252 (mp) cc_final: 0.8007 (mp)
REVERT: B   59 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7389 (m-10)
REVERT: B  210 LEU cc_start: 0.8470 (tp) cc_final: 0.8055 (tp)
REVERT: B  219 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7532 (mpt180)
REVERT: B  223 THR cc_start: 0.7824 (t) cc_final: 0.7576 (p)
REVERT: B  234 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8458 (m-80)
REVERT: B  275 SER cc_start: 0.8001 (t) cc_final: 0.7760 (t)
  outliers start: 28
  outliers final: 21
  residues processed: 231
  average time/residue: 0.2395
  time to fit residues: 73.7344
Evaluate side-chains
  239 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 215
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  304 PHE
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  370 VAL
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  403 ILE
Chi-restraints excluded: chain R residue  423 THR
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain R residue  508 CYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 69 optimal weight:    0.2980
   chunk 106 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0970
   chunk 27 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0000
   chunk 58 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.3982

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.135012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.116367 restraints weight = 12799.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.93
r_work: 0.3300 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9197  Z= 0.161
  Angle     :  0.559   8.957  12475  Z= 0.288
  Chirality :  0.042   0.198   1411
  Planarity :  0.004   0.042   1581
  Dihedral  :  4.337  20.384   1251
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.00 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.18 (0.26), residues: 1134
  helix:  1.28 (0.29), residues: 359
  sheet: -0.27 (0.30), residues: 293
  loop : -1.03 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.023   0.001   PHE S 239 
 TYR   0.012   0.001   TYR A 391 
 ARG   0.003   0.000   ARG B  52 

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 218
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7024 (mt-10)
REVERT: A  216 LYS cc_start: 0.8437 (mppt) cc_final: 0.8132 (mppt)
REVERT: A  246 PHE cc_start: 0.8209 (t80) cc_final: 0.8004 (t80)
REVERT: A  292 ASN cc_start: 0.8304 (t0) cc_final: 0.7976 (t0)
REVERT: A  294 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6842 (mm-40)
REVERT: A  327 GLU cc_start: 0.7913 (mp0) cc_final: 0.7404 (mp0)
REVERT: A  374 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8159 (mtt-85)
REVERT: R  492 ASN cc_start: 0.8438 (m-40) cc_final: 0.8037 (m-40)
REVERT: S   32 PHE cc_start: 0.8275 (m-80) cc_final: 0.7987 (m-80)
REVERT: S  140 MET cc_start: 0.8380 (mmm) cc_final: 0.7733 (mtp)
REVERT: S  174 LEU cc_start: 0.8564 (tp) cc_final: 0.8166 (tp)
REVERT: S  192 MET cc_start: 0.7938 (ptt) cc_final: 0.7689 (ptt)
REVERT: S  202 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7875 (mtm110)
REVERT: S  223 ASP cc_start: 0.7879 (m-30) cc_final: 0.7542 (m-30)
REVERT: S  224 VAL cc_start: 0.8229 (p) cc_final: 0.8016 (t)
REVERT: B   42 ARG cc_start: 0.7364 (ttt-90) cc_final: 0.6914 (ttt-90)
REVERT: B   44 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6534 (mp10)
REVERT: B   55 LEU cc_start: 0.8258 (mp) cc_final: 0.8015 (mp)
REVERT: B   59 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7439 (m-10)
REVERT: B  210 LEU cc_start: 0.8496 (tp) cc_final: 0.8056 (tp)
REVERT: B  219 ARG cc_start: 0.7938 (mmt180) cc_final: 0.7571 (mpt180)
REVERT: B  223 THR cc_start: 0.7795 (t) cc_final: 0.7540 (p)
REVERT: B  234 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8464 (m-80)
REVERT: B  275 SER cc_start: 0.7996 (t) cc_final: 0.7755 (t)
  outliers start: 25
  outliers final: 22
  residues processed: 232
  average time/residue: 0.2514
  time to fit residues: 78.2482
Evaluate side-chains
  245 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 220
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain R residue  231 VAL
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  304 PHE
Chi-restraints excluded: chain R residue  347 TYR
Chi-restraints excluded: chain R residue  370 VAL
Chi-restraints excluded: chain R residue  386 ILE
Chi-restraints excluded: chain R residue  423 THR
Chi-restraints excluded: chain R residue  463 THR
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain R residue  508 CYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  155 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9990
   chunk 107 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0470
   chunk 101 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.134114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.115389 restraints weight = 12818.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.93
r_work: 0.3287 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9197  Z= 0.200
  Angle     :  0.575   8.866  12475  Z= 0.295
  Chirality :  0.042   0.195   1411
  Planarity :  0.004   0.041   1581
  Dihedral  :  4.375  20.154   1251
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.31 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: 1134
  helix:  1.39 (0.29), residues: 352
  sheet: -0.28 (0.30), residues: 283
  loop : -1.00 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.028   0.002   PHE S 239 
 TYR   0.014   0.001   TYR A 391 
 ARG   0.007   0.000   ARG B  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4977.88 seconds
wall clock time: 87 minutes 44.67 seconds (5264.67 seconds total)