Starting phenix.real_space_refine
on Sun Dec 29 21:28:42 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5s_33623/12_2024/7y5s_33623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5s_33623/12_2024/7y5s_33623.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5s_33623/12_2024/7y5s_33623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5s_33623/12_2024/7y5s_33623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5s_33623/12_2024/7y5s_33623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5s_33623/12_2024/7y5s_33623.cif"
  }
  resolution = 3.0
  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=   0.003 sd=   0.040
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      54      5.16       5
     C    7203      2.51       5
     N    2052      2.21       5
     O    2226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 11535
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3845
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 21, 'TRANS': 483}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 7.19, per 1000 atoms: 0.62
  Number of scatterers: 11535
  At special positions: 0
  Unit cell: (92.2236, 93.3215, 148.217, 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      54     16.00
     O    2226      8.00
     N    2052      7.00
     C    7203      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.47
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2670

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 18 sheets defined
      4.4% alpha, 32.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 68
    Processing helix  chain 'A' and resid 270 through 276
      removed outlier: 3.763A  pdb=" N   ALA A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 68
    Processing helix  chain 'B' and resid 270 through 276
      removed outlier: 3.762A  pdb=" N   ALA B 274 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 68
    Processing helix  chain 'C' and resid 270 through 276
      removed outlier: 3.762A  pdb=" N   ALA C 274 " --> pdb=" O   GLY C 270 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ILE C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   ILE A 124 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   VAL A 182 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER A 151 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ASP A 184 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 153 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL A 224 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   HIS A 186 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL A 226 " --> pdb=" O   HIS A 186 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY A 188 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASN A 228 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 9.355A  pdb=" N   ARG A 220 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
      removed outlier: 10.525A  pdb=" N   ASP A 251 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR A 222 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   MET A 253 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL A 224 " --> pdb=" O   MET A 253 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   GLN A 255 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL A 226 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   SER A 248 " --> pdb=" O   LYS A 292 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   GLU A 294 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR A 250 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ASN A 296 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   CYS A 252 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE A 298 " --> pdb=" O   CYS A 252 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   CYS A 254 " --> pdb=" O   PHE A 298 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 139
      removed outlier: 6.799A  pdb=" N   LEU A 173 " --> pdb=" O   PRO A 134 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   PHE A 136 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   GLN A 175 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA A 138 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE A 194 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   PHE A 196 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLN A 175 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ASN A 198 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP A 232 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLY A 263 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL A 237 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU A 307 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ARG A 331 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS A 309 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   ILE A 333 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP A 311 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL A 328 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   VAL A 353 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU A 330 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217
      removed outlier: 3.555A  pdb=" N   THR A 216 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS A 245 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA A 286 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG A 316 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL A 288 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   CYS A 318 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   GLN A 339 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   GLY A 315 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   TYR A 338 " --> pdb=" O   MET A 368 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 394
      removed outlier: 3.772A  pdb=" N   GLY B 416 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLY A 432 " --> pdb=" O   TRP B 419 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TRP A 429 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLN A 448 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LEU A 431 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   SER B 491 " --> pdb=" O   LEU C 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 492
      removed outlier: 6.306A  pdb=" N   SER A 491 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   GLY B 465 " --> pdb=" O   ILE C 456 " (cutoff:3.500A)
      removed outlier: 8.743A  pdb=" N   SER C 458 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   GLN B 467 " --> pdb=" O   SER C 458 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU C 431 " --> pdb=" O   VAL C 446 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   GLN C 448 " --> pdb=" O   TRP C 429 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   TRP C 429 " --> pdb=" O   GLN C 448 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ALA A 417 " --> pdb=" O   ILE C 430 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   GLY C 432 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   TRP A 419 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   ARG C 434 " --> pdb=" O   TRP A 419 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE A 421 " --> pdb=" O   ARG C 434 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY A 416 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 391 through 394
      removed outlier: 3.771A  pdb=" N   GLY C 416 " --> pdb=" O   ILE C 410 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY B 432 " --> pdb=" O   TRP C 419 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   TRP B 429 " --> pdb=" O   GLN B 448 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLN B 448 " --> pdb=" O   TRP B 429 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU B 431 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   GLY A 465 " --> pdb=" O   ILE B 456 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   SER B 458 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN A 467 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 502 through 503
    Processing sheet with id=AA9, first strand: chain 'A' and resid 523 through 524
      removed outlier: 6.963A  pdb=" N   ASN A 523 " --> pdb=" O   ILE B 514 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 74
      removed outlier: 6.062A  pdb=" N   VAL B  73 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   ILE B 124 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 74
      removed outlier: 6.062A  pdb=" N   VAL B  73 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   VAL B 182 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER B 151 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASP B 184 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU B 153 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL B 224 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   HIS B 186 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL B 226 " --> pdb=" O   HIS B 186 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY B 188 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASN B 228 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 9.356A  pdb=" N   ARG B 220 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 10.526A  pdb=" N   ASP B 251 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR B 222 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   MET B 253 " --> pdb=" O   THR B 222 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL B 224 " --> pdb=" O   MET B 253 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLN B 255 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL B 226 " --> pdb=" O   GLN B 255 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   SER B 248 " --> pdb=" O   LYS B 292 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   GLU B 294 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR B 250 " --> pdb=" O   GLU B 294 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   ASN B 296 " --> pdb=" O   THR B 250 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   CYS B 252 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE B 298 " --> pdb=" O   CYS B 252 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   CYS B 254 " --> pdb=" O   PHE B 298 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 347 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 139
      removed outlier: 6.799A  pdb=" N   LEU B 173 " --> pdb=" O   PRO B 134 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE B 136 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   GLN B 175 " --> pdb=" O   PHE B 136 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA B 138 " --> pdb=" O   GLN B 175 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE B 194 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU B 173 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   PHE B 196 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLN B 175 " --> pdb=" O   PHE B 196 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   ASN B 198 " --> pdb=" O   GLN B 175 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASP B 232 " --> pdb=" O   ARG B 192 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 237 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 307 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ARG B 331 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS B 309 " --> pdb=" O   ARG B 331 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   ILE B 333 " --> pdb=" O   HIS B 309 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP B 311 " --> pdb=" O   ILE B 333 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL B 328 " --> pdb=" O   ASN B 351 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   VAL B 353 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU B 330 " --> pdb=" O   VAL B 353 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 217
      removed outlier: 3.556A  pdb=" N   THR B 216 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS B 245 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ALA B 286 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG B 316 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL B 288 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   CYS B 318 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   GLN B 339 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   GLY B 315 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   TYR B 338 " --> pdb=" O   MET B 368 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 523 through 524
      removed outlier: 6.965A  pdb=" N   ASN B 523 " --> pdb=" O   ILE C 514 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL C  73 " --> pdb=" O   PHE C 115 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   ILE C 124 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL C  73 " --> pdb=" O   PHE C 115 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   VAL C 182 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER C 151 " --> pdb=" O   VAL C 182 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASP C 184 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU C 153 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL C 224 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   HIS C 186 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL C 226 " --> pdb=" O   HIS C 186 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   GLY C 188 " --> pdb=" O   VAL C 226 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ASN C 228 " --> pdb=" O   GLY C 188 " (cutoff:3.500A)
      removed outlier: 9.354A  pdb=" N   ARG C 220 " --> pdb=" O   PHE C 249 " (cutoff:3.500A)
      removed outlier: 10.524A  pdb=" N   ASP C 251 " --> pdb=" O   ARG C 220 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR C 222 " --> pdb=" O   ASP C 251 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   MET C 253 " --> pdb=" O   THR C 222 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL C 224 " --> pdb=" O   MET C 253 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLN C 255 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL C 226 " --> pdb=" O   GLN C 255 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   SER C 248 " --> pdb=" O   LYS C 292 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   GLU C 294 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   THR C 250 " --> pdb=" O   GLU C 294 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASN C 296 " --> pdb=" O   THR C 250 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   CYS C 252 " --> pdb=" O   ASN C 296 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE C 298 " --> pdb=" O   CYS C 252 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   CYS C 254 " --> pdb=" O   PHE C 298 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C 347 " --> pdb=" O   VAL C 324 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 134 through 139
      removed outlier: 6.798A  pdb=" N   LEU C 173 " --> pdb=" O   PRO C 134 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE C 136 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   GLN C 175 " --> pdb=" O   PHE C 136 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   ALA C 138 " --> pdb=" O   GLN C 175 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   GLY C 193 " --> pdb=" O   THR C 170 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP C 232 " --> pdb=" O   ARG C 192 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY C 263 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL C 237 " --> pdb=" O   TRP C 267 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU C 307 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ARG C 331 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS C 309 " --> pdb=" O   ARG C 331 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ILE C 333 " --> pdb=" O   HIS C 309 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP C 311 " --> pdb=" O   ILE C 333 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL C 328 " --> pdb=" O   ASN C 351 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   VAL C 353 " --> pdb=" O   VAL C 328 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   LEU C 330 " --> pdb=" O   VAL C 353 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 216 through 217
      removed outlier: 3.555A  pdb=" N   THR C 216 " --> pdb=" O   SER C 243 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   HIS C 245 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ALA C 286 " --> pdb=" O   GLN C 314 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG C 316 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL C 288 " --> pdb=" O   ARG C 316 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   CYS C 318 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   GLN C 339 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   GLY C 315 " --> pdb=" O   GLN C 339 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   TYR C 338 " --> pdb=" O   MET C 368 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    648 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: 4.21

  Time building geometry restraints manager: 2.95 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: 3903
        1.34 -     1.46: 2240
        1.46 -     1.57: 5593
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 11820
  Sorted by residual:
  bond pdb=" CB  PRO B 277 "
       pdb=" CG  PRO B 277 "
    ideal  model  delta    sigma   weight residual
    1.492  1.569 -0.077 5.00e-02 4.00e+02 2.38e+00
  bond pdb=" CB  PRO A 277 "
       pdb=" CG  PRO A 277 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.34e+00
  bond pdb=" CB  PRO C 277 "
       pdb=" CG  PRO C 277 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.33e+00
  bond pdb=" CB  ASP C 396 "
       pdb=" CG  ASP C 396 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.26e+00
  bond pdb=" CB  ASP B 396 "
       pdb=" CG  ASP B 396 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.22e+00
  ... (remaining 11815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 15584
        1.53 -     3.05: 417
        3.05 -     4.58: 79
        4.58 -     6.10: 15
        6.10 -     7.63: 6
  Bond angle restraints: 16101
  Sorted by residual:
  angle pdb=" N   ILE B 521 "
        pdb=" CA  ILE B 521 "
        pdb=" C   ILE B 521 "
      ideal   model   delta    sigma   weight residual
     113.53  109.52    4.01 9.80e-01 1.04e+00 1.67e+01
  angle pdb=" N   ILE C 521 "
        pdb=" CA  ILE C 521 "
        pdb=" C   ILE C 521 "
      ideal   model   delta    sigma   weight residual
     113.53  109.56    3.97 9.80e-01 1.04e+00 1.64e+01
  angle pdb=" N   ILE A 521 "
        pdb=" CA  ILE A 521 "
        pdb=" C   ILE A 521 "
      ideal   model   delta    sigma   weight residual
     113.53  109.57    3.96 9.80e-01 1.04e+00 1.63e+01
  angle pdb=" C   PHE B 499 "
        pdb=" N   THR B 500 "
        pdb=" CA  THR B 500 "
      ideal   model   delta    sigma   weight residual
     121.54  129.17   -7.63 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   PHE A 499 "
        pdb=" N   THR A 500 "
        pdb=" CA  THR A 500 "
      ideal   model   delta    sigma   weight residual
     121.54  129.15   -7.61 1.91e+00 2.74e-01 1.59e+01
  ... (remaining 16096 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.65: 6205
       15.65 -    31.30: 429
       31.30 -    46.95: 119
       46.95 -    62.60: 12
       62.60 -    78.25: 12
  Dihedral angle restraints: 6777
    sinusoidal: 2541
      harmonic: 4236
  Sorted by residual:
  dihedral pdb=" CA  GLU C 156 "
           pdb=" C   GLU C 156 "
           pdb=" N   PRO C 157 "
           pdb=" CA  PRO C 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLU B 156 "
           pdb=" C   GLU B 156 "
           pdb=" N   PRO B 157 "
           pdb=" CA  PRO B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.89  -21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  GLU A 156 "
           pdb=" C   GLU A 156 "
           pdb=" N   PRO A 157 "
           pdb=" CA  PRO A 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.92  -21.08     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 6774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1261
       0.050 -    0.099: 343
       0.099 -    0.149: 127
       0.149 -    0.198: 0
       0.198 -    0.248: 3
  Chirality restraints: 1734
  Sorted by residual:
  chirality pdb=" CB  ILE B  70 "
            pdb=" CA  ILE B  70 "
            pdb=" CG1 ILE B  70 "
            pdb=" CG2 ILE B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  ILE C  70 "
            pdb=" CA  ILE C  70 "
            pdb=" CG1 ILE C  70 "
            pdb=" CG2 ILE C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CB  ILE A  70 "
            pdb=" CA  ILE A  70 "
            pdb=" CG1 ILE A  70 "
            pdb=" CG2 ILE A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 1731 not shown)

  Planarity restraints: 2136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 276 "   -0.055 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        pdb=" N   PRO B 277 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 277 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 277 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 276 "    0.055 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO C 277 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C 277 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 277 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 276 "   -0.055 5.00e-02 4.00e+02   8.27e-02 1.10e+01
        pdb=" N   PRO A 277 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 2133 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 547
        2.73 -     3.27: 11434
        3.27 -     3.81: 20072
        3.81 -     4.36: 25594
        4.36 -     4.90: 43687
  Nonbonded interactions: 101334
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 278 "
            pdb=" OE1 GLU A 283 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER C 278 "
            pdb=" OE1 GLU C 283 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER B 278 "
            pdb=" OE1 GLU B 283 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   GLY A 404 "
            pdb=" NH2 ARG C 434 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" NH2 ARG B 434 "
            pdb=" O   GLY C 404 "
     model   vdw
     2.246 3.120
  ... (remaining 101329 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.600
  Find NCS groups from input model:        0.340
  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:             0.010
  Load rotamer database and sin/cos tables:12.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
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   0.077  11820  Z= 0.173
  Angle     :  0.626   7.630  16101  Z= 0.356
  Chirality :  0.049   0.248   1734
  Planarity :  0.005   0.083   2136
  Dihedral  : 12.391  78.248   4107
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.19), residues: 1509
  helix:  3.94 (0.65), residues: 48
  sheet: -0.28 (0.28), residues: 390
  loop : -2.27 (0.15), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 419 
 HIS   0.002   0.001   HIS C 186 
 PHE   0.011   0.001   PHE C 179 
 TYR   0.014   0.001   TYR A 374 
 ARG   0.003   0.000   ARG B 225 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 ILE cc_start: 0.6749 (mt) cc_final: 0.6536 (mt)
REVERT: A  289 TYR cc_start: 0.8328 (p90) cc_final: 0.8088 (p90)
REVERT: A  293 HIS cc_start: 0.7395 (m170) cc_final: 0.7056 (m170)
REVERT: B  385 LEU cc_start: 0.8825 (mt) cc_final: 0.8609 (mt)
REVERT: B  470 THR cc_start: 0.8136 (m) cc_final: 0.7821 (p)
REVERT: C   76 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6798 (Cg_exo)
REVERT: C  368 MET cc_start: 0.7761 (mtp) cc_final: 0.7378 (mtm)
REVERT: C  451 TYR cc_start: 0.7854 (t80) cc_final: 0.7623 (t80)
REVERT: C  470 THR cc_start: 0.8211 (m) cc_final: 0.7873 (p)
REVERT: C  519 ASP cc_start: 0.6226 (t0) cc_final: 0.5852 (t0)
  outliers start: 0
  outliers final: 2
  residues processed: 316
  average time/residue: 0.7771
  time to fit residues: 278.2342
Evaluate side-chains
  249 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 247
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain C residue  357 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0970
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 136 optimal weight:    0.8980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 110 GLN
A 242 ASN
A 247 ASN
A 255 GLN
A 291 ASN
A 345 HIS
A 376 GLN
A 402 ASN
A 436 GLN
B  69 ASN
B  89 ASN
B 242 ASN
B 402 ASN
B 436 GLN
C  89 ASN
C 110 GLN
** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 ASN
C 255 GLN
C 290 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN
C 402 ASN
** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 436 GLN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11820  Z= 0.330
  Angle     :  0.696  11.928  16101  Z= 0.380
  Chirality :  0.053   0.209   1734
  Planarity :  0.006   0.058   2136
  Dihedral  :  6.318  71.009   1654
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.69 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 11.22 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.20), residues: 1509
  helix:  3.91 (0.67), residues: 48
  sheet: -0.24 (0.28), residues: 414
  loop : -2.26 (0.15), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 419 
 HIS   0.008   0.002   HIS B 145 
 PHE   0.028   0.002   PHE B 474 
 TYR   0.016   0.002   TYR A 120 
 ARG   0.011   0.001   ARG C 440 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 276
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7454 (ptmt)
REVERT: A  264 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5529 (ttm)
REVERT: A  293 HIS cc_start: 0.7829 (m170) cc_final: 0.7599 (m170)
REVERT: A  301 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8024 (m-30)
REVERT: A  399 ASN cc_start: 0.8313 (t0) cc_final: 0.8095 (t0)
REVERT: A  400 SER cc_start: 0.8027 (m) cc_final: 0.7769 (m)
REVERT: A  470 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8039 (p)
REVERT: B   60 ASN cc_start: 0.7550 (m110) cc_final: 0.7318 (m-40)
REVERT: B  110 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6300 (mt0)
REVERT: B  158 VAL cc_start: 0.7320 (t) cc_final: 0.7005 (t)
REVERT: B  160 TRP cc_start: 0.7396 (t60) cc_final: 0.7174 (t60)
REVERT: B  232 ASP cc_start: 0.6554 (m-30) cc_final: 0.6271 (m-30)
REVERT: B  266 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7142 (mtp)
REVERT: B  293 HIS cc_start: 0.7986 (m170) cc_final: 0.7620 (m-70)
REVERT: B  319 ASN cc_start: 0.8284 (p0) cc_final: 0.8033 (p0)
REVERT: B  385 LEU cc_start: 0.8963 (mt) cc_final: 0.8681 (mp)
REVERT: B  388 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8366 (m)
REVERT: B  400 SER cc_start: 0.8177 (m) cc_final: 0.7948 (m)
REVERT: C  102 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6367 (mpt-90)
REVERT: C  488 SER cc_start: 0.8085 (t) cc_final: 0.7864 (p)
  outliers start: 51
  outliers final: 20
  residues processed: 298
  average time/residue: 0.8567
  time to fit residues: 285.6392
Evaluate side-chains
  275 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 247
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  357 ASP
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  418 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 113 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 136 optimal weight:    0.7980
   chunk 147 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9990
   chunk 135 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 109 optimal weight:    0.2980
   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  60 ASN
A  89 ASN
A 376 GLN
A 414 ASN
B  89 ASN
** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
B 290 ASN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
C  56 GLN
C 145 HIS
C 164 ASN
C 290 ASN
C 376 GLN
C 399 ASN
C 409 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11820  Z= 0.204
  Angle     :  0.617   9.207  16101  Z= 0.330
  Chirality :  0.050   0.169   1734
  Planarity :  0.005   0.049   2136
  Dihedral  :  6.567 126.220   1654
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.09 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.20), residues: 1509
  helix:  3.82 (0.66), residues: 48
  sheet: -0.53 (0.27), residues: 399
  loop : -2.14 (0.16), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 419 
 HIS   0.005   0.001   HIS C 145 
 PHE   0.018   0.001   PHE C 474 
 TYR   0.020   0.001   TYR A 395 
 ARG   0.005   0.001   ARG A 272 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 267
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.7115 (p-80) cc_final: 0.6777 (p-80)
REVERT: A  293 HIS cc_start: 0.7888 (m170) cc_final: 0.7630 (m170)
REVERT: A  301 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8047 (m-30)
REVERT: A  399 ASN cc_start: 0.8389 (t0) cc_final: 0.8127 (t0)
REVERT: A  400 SER cc_start: 0.8052 (m) cc_final: 0.7736 (m)
REVERT: B  110 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6352 (mt0)
REVERT: B  158 VAL cc_start: 0.7449 (t) cc_final: 0.7174 (t)
REVERT: B  266 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7176 (mtp)
REVERT: B  293 HIS cc_start: 0.7948 (m170) cc_final: 0.7575 (m-70)
REVERT: B  319 ASN cc_start: 0.8238 (p0) cc_final: 0.7958 (p0)
REVERT: B  347 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (pp)
REVERT: B  385 LEU cc_start: 0.8890 (mt) cc_final: 0.8645 (mp)
REVERT: B  388 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8396 (m)
REVERT: B  400 SER cc_start: 0.8212 (m) cc_final: 0.7978 (m)
REVERT: B  470 THR cc_start: 0.8341 (p) cc_final: 0.8095 (p)
REVERT: C  102 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6300 (mpt-90)
REVERT: C  385 LEU cc_start: 0.8859 (mt) cc_final: 0.8577 (mp)
  outliers start: 31
  outliers final: 12
  residues processed: 283
  average time/residue: 1.0213
  time to fit residues: 319.8625
Evaluate side-chains
  265 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 247
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0970
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9990
   chunk 144 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 129 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 ASN
B 414 ASN
C 164 ASN
C 290 ASN
C 376 GLN
C 399 ASN
C 409 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11820  Z= 0.204
  Angle     :  0.606  13.594  16101  Z= 0.323
  Chirality :  0.050   0.193   1734
  Planarity :  0.005   0.045   2136
  Dihedral  :  5.545  22.748   1652
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.55 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.20), residues: 1509
  helix:  3.85 (0.66), residues: 48
  sheet: -0.72 (0.27), residues: 390
  loop : -2.08 (0.16), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 419 
 HIS   0.004   0.001   HIS B 145 
 PHE   0.033   0.001   PHE B 474 
 TYR   0.014   0.001   TYR C 235 
 ARG   0.006   0.000   ARG C 316 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 256
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 HIS cc_start: 0.7941 (m170) cc_final: 0.7702 (m170)
REVERT: A  400 SER cc_start: 0.8047 (m) cc_final: 0.7827 (m)
REVERT: B   83 MET cc_start: 0.5956 (tpp) cc_final: 0.5697 (tpt)
REVERT: B  139 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.5695 (mtt-85)
REVERT: B  158 VAL cc_start: 0.7524 (t) cc_final: 0.7278 (t)
REVERT: B  160 TRP cc_start: 0.7572 (t60) cc_final: 0.7293 (t60)
REVERT: B  208 ASN cc_start: 0.7603 (m-40) cc_final: 0.7324 (m-40)
REVERT: B  293 HIS cc_start: 0.7968 (m170) cc_final: 0.7587 (m-70)
REVERT: B  319 ASN cc_start: 0.8241 (p0) cc_final: 0.7952 (p0)
REVERT: B  388 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8216 (m)
REVERT: B  396 ASP cc_start: 0.6782 (t70) cc_final: 0.6544 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8053 (m) cc_final: 0.7779 (m)
REVERT: B  470 THR cc_start: 0.8317 (p) cc_final: 0.8093 (p)
REVERT: C  102 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6237 (mpt-90)
REVERT: C  346 SER cc_start: 0.7674 (t) cc_final: 0.7471 (p)
REVERT: C  368 MET cc_start: 0.7612 (mtp) cc_final: 0.7345 (mtm)
REVERT: C  385 LEU cc_start: 0.8815 (mt) cc_final: 0.8559 (mp)
REVERT: C  388 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8357 (m)
  outliers start: 32
  outliers final: 15
  residues processed: 273
  average time/residue: 0.9265
  time to fit residues: 281.7878
Evaluate side-chains
  257 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 239
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  409 ASN
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0470
   chunk 123 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
A 175 GLN
A 290 ASN
A 399 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 GLN
C 164 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.4853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11820  Z= 0.269
  Angle     :  0.662  13.771  16101  Z= 0.351
  Chirality :  0.051   0.188   1734
  Planarity :  0.005   0.047   2136
  Dihedral  :  5.742  21.599   1650
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.21 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.20), residues: 1509
  helix:  3.83 (0.67), residues: 48
  sheet: -0.70 (0.26), residues: 417
  loop : -2.19 (0.16), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 419 
 HIS   0.005   0.001   HIS C 195 
 PHE   0.023   0.002   PHE B 115 
 TYR   0.020   0.001   TYR C 235 
 ARG   0.005   0.001   ARG A 225 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 244
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7664 (ptmt)
REVERT: A  250 THR cc_start: 0.7696 (p) cc_final: 0.7468 (t)
REVERT: A  293 HIS cc_start: 0.7966 (m170) cc_final: 0.7740 (m170)
REVERT: A  301 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8085 (m-30)
REVERT: A  346 SER cc_start: 0.7553 (t) cc_final: 0.7226 (p)
REVERT: A  400 SER cc_start: 0.8070 (m) cc_final: 0.7738 (m)
REVERT: B   41 VAL cc_start: 0.8144 (m) cc_final: 0.7943 (p)
REVERT: B   83 MET cc_start: 0.6094 (tpp) cc_final: 0.5853 (tpt)
REVERT: B  139 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.5640 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7636 (m-40) cc_final: 0.7350 (m110)
REVERT: B  255 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6957 (tm-30)
REVERT: B  279 SER cc_start: 0.8118 (t) cc_final: 0.7895 (p)
REVERT: B  293 HIS cc_start: 0.7996 (m170) cc_final: 0.7571 (m-70)
REVERT: B  319 ASN cc_start: 0.8247 (p0) cc_final: 0.7979 (p0)
REVERT: B  346 SER cc_start: 0.6843 (t) cc_final: 0.6470 (p)
REVERT: B  347 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7334 (pp)
REVERT: B  388 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8285 (m)
REVERT: B  396 ASP cc_start: 0.6807 (t70) cc_final: 0.6582 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8226 (m) cc_final: 0.8003 (m)
REVERT: B  470 THR cc_start: 0.8280 (p) cc_final: 0.8071 (p)
REVERT: C  102 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6250 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7083 (p-80) cc_final: 0.6624 (p-80)
REVERT: C  258 SER cc_start: 0.6685 (OUTLIER) cc_final: 0.6482 (p)
REVERT: C  385 LEU cc_start: 0.8839 (mt) cc_final: 0.8564 (mp)
REVERT: C  388 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8334 (m)
REVERT: C  519 ASP cc_start: 0.7107 (t0) cc_final: 0.6894 (t0)
  outliers start: 41
  outliers final: 16
  residues processed: 266
  average time/residue: 0.9280
  time to fit residues: 274.0123
Evaluate side-chains
  263 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 239
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  357 ASP
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 130 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 145 optimal weight:    4.9990
   chunk 120 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0970
   chunk 76 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 208 ASN
A 399 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
C 164 ASN
C 208 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.4995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11820  Z= 0.212
  Angle     :  0.638  12.780  16101  Z= 0.336
  Chirality :  0.050   0.178   1734
  Planarity :  0.005   0.045   2136
  Dihedral  :  5.729  21.348   1650
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.04 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.20), residues: 1509
  helix:  3.67 (0.66), residues: 48
  sheet: -0.66 (0.27), residues: 387
  loop : -2.20 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 419 
 HIS   0.004   0.001   HIS B 145 
 PHE   0.019   0.001   PHE B 115 
 TYR   0.020   0.001   TYR C 284 
 ARG   0.005   0.001   ARG B 316 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 245
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7476 (mm)
REVERT: A  301 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8099 (m-30)
REVERT: A  346 SER cc_start: 0.7577 (t) cc_final: 0.7278 (p)
REVERT: A  400 SER cc_start: 0.8097 (m) cc_final: 0.7747 (m)
REVERT: B  110 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6317 (mt0)
REVERT: B  208 ASN cc_start: 0.7631 (m-40) cc_final: 0.7341 (m110)
REVERT: B  235 TYR cc_start: 0.7492 (m-80) cc_final: 0.7237 (m-80)
REVERT: B  279 SER cc_start: 0.8079 (t) cc_final: 0.7858 (p)
REVERT: B  293 HIS cc_start: 0.8004 (m170) cc_final: 0.7608 (m-70)
REVERT: B  319 ASN cc_start: 0.8227 (p0) cc_final: 0.7979 (OUTLIER)
REVERT: B  346 SER cc_start: 0.6861 (t) cc_final: 0.6527 (p)
REVERT: B  388 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8205 (m)
REVERT: B  400 SER cc_start: 0.8234 (m) cc_final: 0.8022 (m)
REVERT: B  470 THR cc_start: 0.8297 (p) cc_final: 0.8073 (p)
REVERT: C  102 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6297 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7070 (p-80) cc_final: 0.6539 (p-80)
REVERT: C  385 LEU cc_start: 0.8836 (mt) cc_final: 0.8580 (mp)
REVERT: C  388 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8341 (m)
  outliers start: 37
  outliers final: 19
  residues processed: 264
  average time/residue: 0.8468
  time to fit residues: 250.6219
Evaluate side-chains
  260 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 236
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  357 ASP
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 82 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 144 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.9102

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
B 422 GLN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.5147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11820  Z= 0.229
  Angle     :  0.634  11.835  16101  Z= 0.338
  Chirality :  0.050   0.184   1734
  Planarity :  0.005   0.048   2136
  Dihedral  :  5.737  21.448   1650
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.12 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.20), residues: 1509
  helix:  3.70 (0.67), residues: 48
  sheet: -0.69 (0.27), residues: 387
  loop : -2.22 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 419 
 HIS   0.007   0.001   HIS A 293 
 PHE   0.017   0.001   PHE A 215 
 TYR   0.014   0.001   TYR C 235 
 ARG   0.006   0.001   ARG A 444 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 241
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (mm)
REVERT: A  301 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8099 (m-30)
REVERT: A  400 SER cc_start: 0.8070 (m) cc_final: 0.7698 (m)
REVERT: B   52 THR cc_start: 0.7148 (p) cc_final: 0.6941 (p)
REVERT: B  139 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.5696 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7627 (m-40) cc_final: 0.7341 (m110)
REVERT: B  235 TYR cc_start: 0.7503 (m-80) cc_final: 0.7224 (m-80)
REVERT: B  319 ASN cc_start: 0.8214 (p0) cc_final: 0.7959 (p0)
REVERT: B  346 SER cc_start: 0.6932 (t) cc_final: 0.6731 (p)
REVERT: B  388 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8241 (m)
REVERT: B  396 ASP cc_start: 0.6882 (t70) cc_final: 0.6651 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8307 (m) cc_final: 0.8087 (m)
REVERT: B  470 THR cc_start: 0.8226 (p) cc_final: 0.8004 (p)
REVERT: C  145 HIS cc_start: 0.7052 (p-80) cc_final: 0.6529 (p-80)
REVERT: C  264 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5395 (tmt)
REVERT: C  385 LEU cc_start: 0.8843 (mt) cc_final: 0.8602 (mp)
  outliers start: 37
  outliers final: 19
  residues processed: 259
  average time/residue: 0.8805
  time to fit residues: 254.5930
Evaluate side-chains
  255 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 232
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  264 MET
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0770
   chunk 91 optimal weight:    0.6980
   chunk 98 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 131 optimal weight:    0.0370
   chunk 138 optimal weight:    0.5980
   chunk 126 optimal weight:    3.9990
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
C 164 ASN
C 208 ASN
C 309 HIS
C 376 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.5227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11820  Z= 0.169
  Angle     :  0.617  12.507  16101  Z= 0.325
  Chirality :  0.049   0.177   1734
  Planarity :  0.004   0.048   2136
  Dihedral  :  5.544  20.011   1650
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.61 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.20), residues: 1509
  helix:  3.63 (0.66), residues: 48
  sheet: -0.76 (0.26), residues: 393
  loop : -2.20 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 419 
 HIS   0.008   0.001   HIS A 293 
 PHE   0.018   0.001   PHE A 215 
 TYR   0.012   0.001   TYR C 235 
 ARG   0.008   0.000   ARG C 316 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 238
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  301 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8065 (m-30)
REVERT: A  346 SER cc_start: 0.7558 (t) cc_final: 0.7269 (p)
REVERT: A  400 SER cc_start: 0.8006 (m) cc_final: 0.7728 (m)
REVERT: B   41 VAL cc_start: 0.8237 (m) cc_final: 0.8032 (p)
REVERT: B  139 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.5587 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7586 (m-40) cc_final: 0.7341 (m110)
REVERT: B  235 TYR cc_start: 0.7474 (m-80) cc_final: 0.7170 (m-80)
REVERT: B  255 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6937 (tm-30)
REVERT: B  280 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7340 (mp)
REVERT: B  319 ASN cc_start: 0.8202 (p0) cc_final: 0.7937 (p0)
REVERT: B  346 SER cc_start: 0.6912 (t) cc_final: 0.6698 (p)
REVERT: B  352 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7637 (p)
REVERT: B  388 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8181 (m)
REVERT: B  400 SER cc_start: 0.8225 (m) cc_final: 0.8007 (m)
REVERT: B  470 THR cc_start: 0.8218 (p) cc_final: 0.7984 (p)
REVERT: C  145 HIS cc_start: 0.7031 (p-80) cc_final: 0.6562 (p-80)
REVERT: C  264 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5519 (tmt)
REVERT: C  368 MET cc_start: 0.7553 (mtp) cc_final: 0.7212 (mtm)
REVERT: C  385 LEU cc_start: 0.8866 (mt) cc_final: 0.8639 (mp)
  outliers start: 36
  outliers final: 17
  residues processed: 260
  average time/residue: 0.8811
  time to fit residues: 256.3886
Evaluate side-chains
  254 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 230
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  264 MET
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    0.1980
   chunk 138 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 142 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 376 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.5303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11820  Z= 0.194
  Angle     :  0.630  11.772  16101  Z= 0.331
  Chirality :  0.049   0.180   1734
  Planarity :  0.005   0.047   2136
  Dihedral  :  5.558  20.319   1650
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.77 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.20), residues: 1509
  helix:  3.59 (0.66), residues: 48
  sheet: -0.76 (0.26), residues: 393
  loop : -2.21 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 419 
 HIS   0.008   0.001   HIS A 293 
 PHE   0.016   0.001   PHE A 215 
 TYR   0.018   0.001   TYR C 235 
 ARG   0.007   0.000   ARG B 316 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 236
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.5336 (tpt) cc_final: 0.5071 (tmm)
REVERT: A  264 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.5282 (tmm)
REVERT: A  301 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8077 (m-30)
REVERT: A  400 SER cc_start: 0.8023 (m) cc_final: 0.7705 (m)
REVERT: B   41 VAL cc_start: 0.8251 (m) cc_final: 0.8028 (p)
REVERT: B  139 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5565 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7588 (m-40) cc_final: 0.7333 (m110)
REVERT: B  235 TYR cc_start: 0.7496 (m-80) cc_final: 0.7203 (m-80)
REVERT: B  280 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7391 (mp)
REVERT: B  319 ASN cc_start: 0.8216 (p0) cc_final: 0.7938 (p0)
REVERT: B  346 SER cc_start: 0.6951 (t) cc_final: 0.6750 (p)
REVERT: B  388 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8181 (m)
REVERT: B  396 ASP cc_start: 0.6713 (t70) cc_final: 0.6501 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8300 (m) cc_final: 0.8086 (m)
REVERT: B  470 THR cc_start: 0.8236 (p) cc_final: 0.8003 (p)
REVERT: C  145 HIS cc_start: 0.7054 (p-80) cc_final: 0.6516 (p-80)
REVERT: C  264 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5408 (tmt)
REVERT: C  385 LEU cc_start: 0.8871 (mt) cc_final: 0.8656 (mp)
  outliers start: 37
  outliers final: 19
  residues processed: 254
  average time/residue: 0.8790
  time to fit residues: 249.2834
Evaluate side-chains
  253 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 229
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  264 MET
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 149 optimal weight:    0.0970
   chunk 137 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 91 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 126 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11820  Z= 0.214
  Angle     :  0.643  11.880  16101  Z= 0.338
  Chirality :  0.050   0.183   1734
  Planarity :  0.005   0.047   2136
  Dihedral  :  5.627  20.501   1650
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.35 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.20), residues: 1509
  helix:  3.62 (0.67), residues: 48
  sheet: -0.79 (0.27), residues: 393
  loop : -2.23 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 419 
 HIS   0.008   0.001   HIS A 293 
 PHE   0.038   0.002   PHE B 474 
 TYR   0.020   0.001   TYR C 235 
 ARG   0.007   0.001   ARG C 316 

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 240
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.5469 (tpt) cc_final: 0.5231 (tmm)
REVERT: A  301 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8093 (m-30)
REVERT: A  400 SER cc_start: 0.8020 (m) cc_final: 0.7737 (m)
REVERT: B   41 VAL cc_start: 0.8271 (m) cc_final: 0.8056 (p)
REVERT: B  139 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.5533 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7587 (m-40) cc_final: 0.7338 (m110)
REVERT: B  235 TYR cc_start: 0.7504 (m-80) cc_final: 0.7160 (m-80)
REVERT: B  253 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4887 (ttp)
REVERT: B  280 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7489 (mt)
REVERT: B  319 ASN cc_start: 0.8205 (p0) cc_final: 0.7919 (p0)
REVERT: B  388 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8206 (m)
REVERT: B  400 SER cc_start: 0.8228 (m) cc_final: 0.7998 (m)
REVERT: B  470 THR cc_start: 0.8225 (p) cc_final: 0.8008 (p)
REVERT: C  145 HIS cc_start: 0.7040 (p-80) cc_final: 0.6489 (p-80)
REVERT: C  385 LEU cc_start: 0.8879 (mt) cc_final: 0.8656 (mp)
  outliers start: 30
  outliers final: 20
  residues processed: 257
  average time/residue: 0.8852
  time to fit residues: 254.0253
Evaluate side-chains
  257 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  253 MET
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  253 MET
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  357 ASP
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    0.0040
   chunk 17 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0170
   chunk 119 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.6036

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
A 463 ASN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.142484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.129227 restraints weight = 16020.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.09
r_work: 0.3614 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.5665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  11820  Z= 0.354
  Angle     :  0.713  11.192  16101  Z= 0.379
  Chirality :  0.053   0.217   1734
  Planarity :  0.006   0.053   2136
  Dihedral  :  6.036  23.897   1650
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.34 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.20), residues: 1509
  helix:  3.53 (0.68), residues: 48
  sheet: -0.87 (0.26), residues: 393
  loop : -2.24 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 419 
 HIS   0.007   0.002   HIS A 293 
 PHE   0.042   0.002   PHE B 474 
 TYR   0.027   0.002   TYR C 235 
 ARG   0.008   0.001   ARG A 444 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4606.33 seconds
wall clock time: 83 minutes 22.86 seconds (5002.86 seconds total)