Starting phenix.real_space_refine
on Sun Mar 10 18:41:36 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6b_13224/03_2024/7p6b_13224.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6b_13224/03_2024/7p6b_13224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6b_13224/03_2024/7p6b_13224.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6b_13224/03_2024/7p6b_13224.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6b_13224/03_2024/7p6b_13224.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6b_13224/03_2024/7p6b_13224.pdb"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      10      5.16       5
     C    2530      2.51       5
     N     760      2.21       5
     O     760      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  348": "OD1" <-> "OD2"
    Residue "A GLU  372": "OE1" <-> "OE2"
    Residue "B TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  348": "OD1" <-> "OD2"
    Residue "B GLU  372": "OE1" <-> "OE2"
    Residue "C TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  348": "OD1" <-> "OD2"
    Residue "C GLU  372": "OE1" <-> "OE2"
    Residue "D TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  348": "OD1" <-> "OD2"
    Residue "D GLU  372": "OE1" <-> "OE2"
    Residue "E TYR  310": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  348": "OD1" <-> "OD2"
    Residue "E GLU  372": "OE1" <-> "OE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 4060
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "B"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "C"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "E"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
  Time building chain proxies: 2.66, per 1000 atoms: 0.66
  Number of scatterers: 4060
  At special positions: 0
  Unit cell: (106.869, 82.151, 43.62, 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      10     16.00
     O     760      8.00
     N     760      7.00
     C    2530      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  - 3.50
        Amino acid           : False - 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: 1.42
  Conformation dependent library (CDL) restraints added in 849.0 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  930

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 53.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 291
      removed outlier: 8.916A  pdb=" N   GLN B 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 10.182A  pdb=" N   ASN C 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 10.269A  pdb=" N   LYS C 281 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   LYS B 280 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   ASP C 283 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU B 282 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   SER C 285 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU B 284 " --> pdb=" O   SER C 285 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL C 287 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   ASN B 286 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 10.053A  pdb=" N   SER C 289 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 9.168A  pdb=" N   GLN B 288 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 10.283A  pdb=" N   CYS C 291 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   LYS B 290 " --> pdb=" O   CYS C 291 " (cutoff:3.500A)
      removed outlier: 8.913A  pdb=" N   GLN A 276 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 10.177A  pdb=" N   ASN B 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 9.247A  pdb=" N   ILE A 278 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 10.261A  pdb=" N   LYS B 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   LYS A 280 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   ASP B 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LEU A 282 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   SER B 285 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A 284 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   VAL B 287 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   ASN A 286 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 10.057A  pdb=" N   SER B 289 " --> pdb=" O   ASN A 286 " (cutoff:3.500A)
      removed outlier: 9.171A  pdb=" N   GLN A 288 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 10.285A  pdb=" N   CYS B 291 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   LYS A 290 " --> pdb=" O   CYS B 291 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   GLN D 276 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE A 277 " --> pdb=" O   GLN D 276 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ILE D 278 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ASN A 279 " --> pdb=" O   ILE D 278 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LYS D 280 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LYS A 281 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL A 287 " --> pdb=" O   ASN D 286 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLN D 288 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   SER A 289 " --> pdb=" O   GLN D 288 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LYS D 290 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   CYS A 291 " --> pdb=" O   LYS D 290 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLN E 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ILE D 277 " --> pdb=" O   GLN E 276 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE E 278 " --> pdb=" O   ILE D 277 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   ASN D 279 " --> pdb=" O   ILE E 278 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LYS E 280 " --> pdb=" O   ASN D 279 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LYS D 281 " --> pdb=" O   LYS E 280 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL D 287 " --> pdb=" O   ASN E 286 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   GLN E 288 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   SER D 289 " --> pdb=" O   GLN E 288 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LYS E 290 " --> pdb=" O   SER D 289 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   CYS D 291 " --> pdb=" O   LYS E 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 298
      removed outlier: 6.393A  pdb=" N   ILE B 297 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE A 297 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 305 through 310
      removed outlier: 6.685A  pdb=" N   SER A 305 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   ILE D 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   GLN A 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   TYR D 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   SER D 305 " --> pdb=" O   VAL E 306 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   ILE E 308 " --> pdb=" O   SER D 305 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   GLN D 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   TYR E 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL D 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.694A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL D 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.409A  pdb=" N   VAL B 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   LYS C 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   SER B 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   VAL A 318 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   LYS B 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   SER A 320 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.499A  pdb=" N   ILE B 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.359A  pdb=" N   GLU A 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   SER D 341 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LYS A 340 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LYS D 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   GLU A 342 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   ASP D 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU A 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   GLU D 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   SER E 341 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LYS D 340 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   LYS E 343 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   GLU D 342 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ASP E 345 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU D 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 349 through 354
      removed outlier: 6.391A  pdb=" N   VAL A 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   LYS D 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   SER A 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL D 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   LYS E 353 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   SER D 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362
      removed outlier: 8.759A  pdb=" N   LEU B 357 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 9.421A  pdb=" N   ILE C 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ASN B 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   HIS C 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR B 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 8.764A  pdb=" N   LEU A 357 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 9.425A  pdb=" N   ILE B 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ASN A 359 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   HIS B 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   THR A 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ASP A 358 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASN D 359 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ASP D 358 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ASN E 359 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.302A  pdb=" N   LYS B 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.801A  pdb=" N   GLU C 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILE B 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   HIS C 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   THR B 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   LEU C 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LYS B 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   PHE C 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   THR B 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   HIS B 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LYS A 370 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS D 370 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)

    88 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1355
        1.34 -     1.46: 649
        1.46 -     1.58: 2101
        1.58 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 4115
  Sorted by residual:
  bond pdb=" CG  GLN B 288 "
       pdb=" CD  GLN B 288 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.39e+00
  bond pdb=" CG  GLN A 288 "
       pdb=" CD  GLN A 288 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.39e+00
  bond pdb=" CG  GLN D 288 "
       pdb=" CD  GLN D 288 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.39e+00
  bond pdb=" CG  GLN E 288 "
       pdb=" CD  GLN E 288 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.36e+00
  bond pdb=" CG  GLN C 288 "
       pdb=" CD  GLN C 288 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.30e+00
  ... (remaining 4110 not shown)

  Histogram of bond angle deviations from ideal:
      102.44 -   108.20: 269
      108.20 -   113.96: 2317
      113.96 -   119.73: 976
      119.73 -   125.49: 1888
      125.49 -   131.25: 45
  Bond angle restraints: 5495
  Sorted by residual:
  angle pdb=" C   SER E 324 "
        pdb=" N   LEU E 325 "
        pdb=" CA  LEU E 325 "
      ideal   model   delta    sigma   weight residual
     122.64  117.01    5.63 1.77e+00 3.19e-01 1.01e+01
  angle pdb=" C   SER B 324 "
        pdb=" N   LEU B 325 "
        pdb=" CA  LEU B 325 "
      ideal   model   delta    sigma   weight residual
     122.64  117.05    5.59 1.77e+00 3.19e-01 9.99e+00
  angle pdb=" C   SER A 324 "
        pdb=" N   LEU A 325 "
        pdb=" CA  LEU A 325 "
      ideal   model   delta    sigma   weight residual
     122.64  117.05    5.59 1.77e+00 3.19e-01 9.98e+00
  angle pdb=" C   SER C 324 "
        pdb=" N   LEU C 325 "
        pdb=" CA  LEU C 325 "
      ideal   model   delta    sigma   weight residual
     122.64  117.05    5.59 1.77e+00 3.19e-01 9.97e+00
  angle pdb=" C   SER D 324 "
        pdb=" N   LEU D 325 "
        pdb=" CA  LEU D 325 "
      ideal   model   delta    sigma   weight residual
     122.64  117.08    5.56 1.77e+00 3.19e-01 9.88e+00
  ... (remaining 5490 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.06: 2260
       14.06 -    28.12: 165
       28.12 -    42.18: 65
       42.18 -    56.24: 25
       56.24 -    70.29: 10
  Dihedral angle restraints: 2525
    sinusoidal: 1055
      harmonic: 1470
  Sorted by residual:
  dihedral pdb=" N   LYS C 343 "
           pdb=" CA  LYS C 343 "
           pdb=" CB  LYS C 343 "
           pdb=" CG  LYS C 343 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -100.81   40.81     3      1.50e+01 4.44e-03 7.28e+00
  dihedral pdb=" N   LYS B 343 "
           pdb=" CA  LYS B 343 "
           pdb=" CB  LYS B 343 "
           pdb=" CG  LYS B 343 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -100.80   40.80     3      1.50e+01 4.44e-03 7.28e+00
  dihedral pdb=" N   LYS A 343 "
           pdb=" CA  LYS A 343 "
           pdb=" CB  LYS A 343 "
           pdb=" CG  LYS A 343 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -100.79   40.79     3      1.50e+01 4.44e-03 7.28e+00
  ... (remaining 2522 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 600
       0.148 -    0.296: 10
       0.296 -    0.444: 0
       0.444 -    0.592: 0
       0.592 -    0.740: 5
  Chirality restraints: 615
  Sorted by residual:
  chirality pdb=" CG  LEU E 325 "
            pdb=" CB  LEU E 325 "
            pdb=" CD1 LEU E 325 "
            pdb=" CD2 LEU E 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CG  LEU D 325 "
            pdb=" CB  LEU D 325 "
            pdb=" CD1 LEU D 325 "
            pdb=" CD2 LEU D 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.36e+01
  chirality pdb=" CG  LEU B 325 "
            pdb=" CB  LEU B 325 "
            pdb=" CD1 LEU B 325 "
            pdb=" CD2 LEU B 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.36e+01
  ... (remaining 612 not shown)

  Planarity restraints: 705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 349 "    0.130 9.50e-02 1.11e+02   5.87e-02 2.64e+00
        pdb=" NE  ARG C 349 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 349 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 349 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 349 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 349 "    0.131 9.50e-02 1.11e+02   5.91e-02 2.64e+00
        pdb=" NE  ARG B 349 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 349 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 349 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 349 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 349 "    0.130 9.50e-02 1.11e+02   5.88e-02 2.63e+00
        pdb=" NE  ARG D 349 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 349 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 349 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 349 "    0.001 2.00e-02 2.50e+03
  ... (remaining 702 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 513
        2.78 -     3.31: 3547
        3.31 -     3.84: 6897
        3.84 -     4.37: 8246
        4.37 -     4.90: 15814
  Nonbonded interactions: 35017
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 295 "
            pdb=" OH  TYR D 310 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ASP E 295 "
            pdb=" OH  TYR E 310 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ASP C 295 "
            pdb=" OH  TYR C 310 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ASP A 295 "
            pdb=" OH  TYR A 310 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" O   ASP B 295 "
            pdb=" OH  TYR B 310 "
     model   vdw
     2.247 2.440
  ... (remaining 35012 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.750
  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:          8.020
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     16.200
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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      :  0.004   0.045   4115  Z= 0.244
  Angle     :  0.748   7.103   5495  Z= 0.377
  Chirality :  0.090   0.740    615
  Planarity :  0.006   0.059    705
  Dihedral  : 13.804  70.294   1595
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.60 (0.27), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 374 
 PHE   0.003   0.001   PHE B 378 
 TYR   0.006   0.002   TYR A 310 
 ARG   0.013   0.003   ARG C 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8051 (tt) cc_final: 0.7717 (mp)
REVERT: B  376 LEU cc_start: 0.8087 (tt) cc_final: 0.7779 (mp)
REVERT: C  376 LEU cc_start: 0.8126 (tt) cc_final: 0.7808 (mp)
REVERT: D  342 GLU cc_start: 0.7490 (tt0) cc_final: 0.7283 (tt0)
REVERT: D  376 LEU cc_start: 0.8072 (tt) cc_final: 0.7742 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.9758
  time to fit residues: 120.6464
Evaluate side-chains
  93 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.0040
   chunk 37 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.5796

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
B 276 GLN
C 279 ASN
C 296 ASN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4115  Z= 0.263
  Angle     :  0.563   5.009   5495  Z= 0.289
  Chirality :  0.051   0.141    615
  Planarity :  0.003   0.027    705
  Dihedral  :  5.541  13.456    550
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.60 %
    Favored  : 90.54 %
  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: -2.42 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.004   0.001   PHE E 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.001   0.001   ARG C 349 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8298 (tt) cc_final: 0.7990 (mp)
REVERT: A  379 ARG cc_start: 0.5930 (mtp85) cc_final: 0.5383 (tpp80)
REVERT: B  376 LEU cc_start: 0.8264 (tt) cc_final: 0.7961 (mp)
REVERT: D  376 LEU cc_start: 0.8228 (tt) cc_final: 0.7964 (mp)
  outliers start: 4
  outliers final: 0
  residues processed: 112
  average time/residue: 1.0056
  time to fit residues: 117.0037
Evaluate side-chains
  101 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 279 ASN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4115  Z= 0.268
  Angle     :  0.563   6.395   5495  Z= 0.289
  Chirality :  0.051   0.137    615
  Planarity :  0.003   0.043    705
  Dihedral  :  5.596  14.071    550
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.47 %
    Favored  : 86.45 %
  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: -2.43 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.002   0.000   ARG D 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A  379 ARG cc_start: 0.5836 (mtp85) cc_final: 0.5629 (ttp80)
REVERT: B  376 LEU cc_start: 0.8334 (tt) cc_final: 0.8053 (mp)
REVERT: B  379 ARG cc_start: 0.6215 (tpp-160) cc_final: 0.5203 (tpp-160)
REVERT: D  376 LEU cc_start: 0.8256 (tt) cc_final: 0.8004 (mp)
REVERT: D  379 ARG cc_start: 0.5861 (mtp85) cc_final: 0.5266 (tpp80)
  outliers start: 5
  outliers final: 1
  residues processed: 106
  average time/residue: 1.0585
  time to fit residues: 116.3253
Evaluate side-chains
  103 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  338 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 23 optimal weight:    0.2980
   chunk 5 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    3.0588

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 288 GLN
B 276 GLN
C 279 ASN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4115  Z= 0.289
  Angle     :  0.579   6.951   5495  Z= 0.295
  Chirality :  0.051   0.138    615
  Planarity :  0.003   0.033    705
  Dihedral  :  5.644  13.719    550
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.84 %
    Favored  : 83.44 %
  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: -2.38 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.004   0.001   PHE B 346 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.005   0.001   ARG C 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8415 (tm) cc_final: 0.8142 (mt)
REVERT: A  379 ARG cc_start: 0.5944 (mtp85) cc_final: 0.5625 (ttp80)
REVERT: B  288 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7077 (mm110)
REVERT: B  376 LEU cc_start: 0.8236 (tt) cc_final: 0.7965 (mp)
REVERT: B  379 ARG cc_start: 0.6262 (tpp-160) cc_final: 0.5241 (tpp-160)
REVERT: C  277 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8358 (mm)
REVERT: D  376 LEU cc_start: 0.8251 (tt) cc_final: 0.8024 (mp)
REVERT: E  376 LEU cc_start: 0.8390 (tt) cc_final: 0.8103 (mp)
REVERT: E  379 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6012 (ttp80)
  outliers start: 8
  outliers final: 1
  residues processed: 109
  average time/residue: 1.0212
  time to fit residues: 115.5600
Evaluate side-chains
  108 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain E residue  379 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0980
   overall best weight:    5.0188

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
C 279 ASN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4115  Z= 0.431
  Angle     :  0.646   5.916   5495  Z= 0.335
  Chirality :  0.053   0.153    615
  Planarity :  0.004   0.036    705
  Dihedral  :  5.944  14.982    550
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.84 %
    Favored  : 82.37 %
  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: -2.39 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 299 
 PHE   0.006   0.001   PHE E 346 
 TYR   0.005   0.002   TYR C 310 
 ARG   0.007   0.001   ARG D 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.6914 (mm110)
REVERT: A  376 LEU cc_start: 0.8426 (tm) cc_final: 0.8188 (mt)
REVERT: A  379 ARG cc_start: 0.6013 (mtp85) cc_final: 0.5736 (ttp80)
REVERT: B  288 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7002 (mm110)
REVERT: B  376 LEU cc_start: 0.8265 (tt) cc_final: 0.7989 (mp)
REVERT: B  379 ARG cc_start: 0.6231 (tpp-160) cc_final: 0.5256 (tpp-160)
REVERT: C  277 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8317 (mm)
REVERT: C  288 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7335 (mt0)
REVERT: D  376 LEU cc_start: 0.8334 (tt) cc_final: 0.8091 (mp)
REVERT: E  376 LEU cc_start: 0.8403 (tt) cc_final: 0.8160 (mp)
  outliers start: 13
  outliers final: 1
  residues processed: 109
  average time/residue: 1.0285
  time to fit residues: 116.3216
Evaluate side-chains
  109 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 GLN
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain D residue  338 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
C 279 ASN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4115  Z= 0.304
  Angle     :  0.582   6.216   5495  Z= 0.299
  Chirality :  0.051   0.136    615
  Planarity :  0.003   0.028    705
  Dihedral  :  5.739  14.074    550
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.70 %
    Favored  : 81.51 %
  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: -2.37 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.004   0.001   PHE B 346 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.003   0.001   ARG C 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8402 (tm) cc_final: 0.8168 (mt)
REVERT: B  288 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7094 (mm110)
REVERT: B  376 LEU cc_start: 0.8209 (tt) cc_final: 0.7978 (mp)
REVERT: C  277 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8307 (mm)
REVERT: C  288 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7359 (mt0)
REVERT: C  379 ARG cc_start: 0.3807 (OUTLIER) cc_final: 0.2808 (mtm110)
REVERT: D  288 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7161 (mm110)
REVERT: D  376 LEU cc_start: 0.8270 (tt) cc_final: 0.8041 (mp)
REVERT: E  376 LEU cc_start: 0.8362 (tt) cc_final: 0.8136 (mp)
  outliers start: 13
  outliers final: 1
  residues processed: 109
  average time/residue: 1.0163
  time to fit residues: 115.0681
Evaluate side-chains
  112 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  288 GLN
Chi-restraints excluded: chain D residue  338 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0170
   chunk 48 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    0.1980
   chunk 14 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    2.4424

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4115  Z= 0.244
  Angle     :  0.567   8.249   5495  Z= 0.287
  Chirality :  0.052   0.172    615
  Planarity :  0.003   0.027    705
  Dihedral  :  5.622  13.549    550
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.77 %
    Favored  : 80.86 %
  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: -2.34 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.003   0.001   PHE B 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.000   ARG C 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8391 (tm) cc_final: 0.8165 (mt)
REVERT: C  288 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7501 (mt0)
REVERT: C  379 ARG cc_start: 0.4055 (OUTLIER) cc_final: 0.3291 (mpp-170)
REVERT: D  376 LEU cc_start: 0.8257 (tt) cc_final: 0.8037 (mp)
REVERT: E  376 LEU cc_start: 0.8341 (tt) cc_final: 0.8099 (mp)
  outliers start: 11
  outliers final: 2
  residues processed: 109
  average time/residue: 0.9132
  time to fit residues: 103.2161
Evaluate side-chains
  109 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 37 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0670
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    3.6126

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4115  Z= 0.332
  Angle     :  0.620   7.037   5495  Z= 0.313
  Chirality :  0.052   0.148    615
  Planarity :  0.003   0.030    705
  Dihedral  :  5.805  14.070    550
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.77 %
    Favored  : 81.29 %
  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: -2.31 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.004   0.001   PHE B 346 
 TYR   0.006   0.002   TYR C 310 
 ARG   0.003   0.001   ARG C 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8400 (tm) cc_final: 0.8174 (mt)
REVERT: C  277 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8297 (mm)
REVERT: C  288 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7465 (mt0)
REVERT: C  379 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.2852 (mtm110)
REVERT: D  376 LEU cc_start: 0.8297 (tt) cc_final: 0.8082 (mp)
REVERT: E  376 LEU cc_start: 0.8370 (tt) cc_final: 0.8140 (mp)
  outliers start: 9
  outliers final: 2
  residues processed: 110
  average time/residue: 1.0488
  time to fit residues: 119.6996
Evaluate side-chains
  111 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4115  Z= 0.358
  Angle     :  0.636   6.939   5495  Z= 0.320
  Chirality :  0.053   0.183    615
  Planarity :  0.003   0.030    705
  Dihedral  :  5.848  14.428    550
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.20 %
    Favored  : 81.08 %
  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: -2.31 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.005   0.001   PHE B 346 
 TYR   0.006   0.002   TYR C 310 
 ARG   0.003   0.001   ARG C 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8404 (tm) cc_final: 0.8177 (mt)
REVERT: C  277 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8304 (mm)
REVERT: C  288 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7457 (mt0)
REVERT: C  379 ARG cc_start: 0.4330 (OUTLIER) cc_final: 0.3610 (mtm180)
REVERT: D  376 LEU cc_start: 0.8293 (tt) cc_final: 0.8084 (mp)
REVERT: E  376 LEU cc_start: 0.8380 (tt) cc_final: 0.8141 (mp)
  outliers start: 8
  outliers final: 2
  residues processed: 110
  average time/residue: 1.0076
  time to fit residues: 115.0447
Evaluate side-chains
  112 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   4115  Z= 0.535
  Angle     :  0.735   8.460   5495  Z= 0.370
  Chirality :  0.057   0.262    615
  Planarity :  0.004   0.034    705
  Dihedral  :  6.146  15.815    550
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.63 %
    Favored  : 81.08 %
  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: -2.31 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 299 
 PHE   0.007   0.002   PHE B 346 
 TYR   0.005   0.002   TYR C 310 
 ARG   0.004   0.001   ARG C 379 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8420 (tm) cc_final: 0.8177 (mt)
REVERT: C  277 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8358 (mm)
REVERT: C  288 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7459 (mt0)
REVERT: C  379 ARG cc_start: 0.4354 (OUTLIER) cc_final: 0.3984 (mtm-85)
REVERT: D  376 LEU cc_start: 0.8343 (tt) cc_final: 0.8113 (mp)
REVERT: E  376 LEU cc_start: 0.8413 (tt) cc_final: 0.8177 (mp)
  outliers start: 6
  outliers final: 2
  residues processed: 107
  average time/residue: 1.0414
  time to fit residues: 115.5544
Evaluate side-chains
  112 residues out of total 465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  338 GLU
Chi-restraints excluded: chain E residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.128495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.115729 restraints weight = 4283.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.32
r_work: 0.3669 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3576 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4115  Z= 0.232
  Angle     :  0.583   6.855   5495  Z= 0.291
  Chirality :  0.052   0.200    615
  Planarity :  0.003   0.028    705
  Dihedral  :  5.663  13.913    550
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.42 %
    Favored  : 81.08 %
  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: -2.28 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 299 
 PHE   0.003   0.001   PHE B 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.000   ARG C 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2347.21 seconds
wall clock time: 42 minutes 11.53 seconds (2531.53 seconds total)