Starting phenix.real_space_refine
on Tue Feb 11 04:11:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p6b_13224/02_2025/7p6b_13224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p6b_13224/02_2025/7p6b_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/cci-nas-00/data/ceres_data/7p6b_13224/02_2025/7p6b_13224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p6b_13224/02_2025/7p6b_13224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p6b_13224/02_2025/7p6b_13224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p6b_13224/02_2025/7p6b_13224.cif"
  }
  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. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4060
  Number of models: 1
  Model: ""
    Number of chains: 1
    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}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.46, per 1000 atoms: 0.61
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 518.4 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: 0.59
  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: 0.99

  Time building geometry restraints manager: 1.01 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:
        0.00 -     1.42: 5254
        1.42 -     2.84: 166
        2.84 -     4.26: 50
        4.26 -     5.68: 15
        5.68 -     7.10: 10
  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 3.040
  nonbonded pdb=" O   ASP E 295 "
            pdb=" OH  TYR E 310 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   ASP C 295 "
            pdb=" OH  TYR C 310 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   ASP A 295 "
            pdb=" OH  TYR A 310 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ASP B 295 "
            pdb=" OH  TYR B 310 "
     model   vdw
     2.247 3.040
  ... (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
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             2.170
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.210
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:11.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.450
-------------------------------------------------------------------------------
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 to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.479 
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: 1.0294
  time to fit residues: 127.0165
Evaluate side-chains
  93 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 336 GLN
B 276 GLN
B 288 GLN
C 279 ASN
C 296 ASN
C 336 GLN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 336 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.128542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.115403 restraints weight = 4260.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 1.31
r_work: 0.3648 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4115  Z= 0.321
  Angle     :  0.602   5.251   5495  Z= 0.310
  Chirality :  0.052   0.154    615
  Planarity :  0.004   0.030    705
  Dihedral  :  5.689  14.306    550
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.96 %
    Favored  : 91.18 %
  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 E 346 
 TYR   0.007   0.003   TYR A 310 
 ARG   0.001   0.001   ARG B 379 

*********************** 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
  117 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8551 (tt) cc_final: 0.8227 (mp)
REVERT: A  379 ARG cc_start: 0.6496 (mtp85) cc_final: 0.5881 (tpp80)
REVERT: B  376 LEU cc_start: 0.8517 (tt) cc_final: 0.8168 (mp)
REVERT: D  376 LEU cc_start: 0.8473 (tt) cc_final: 0.8168 (mp)
  outliers start: 4
  outliers final: 0
  residues processed: 113
  average time/residue: 1.0663
  time to fit residues: 124.8963
Evaluate side-chains
  100 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 16 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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 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
C 336 GLN
** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN
E 288 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.129924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.117457 restraints weight = 4300.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 1.29
r_work: 0.3690 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3601 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4115  Z= 0.231
  Angle     :  0.540   6.339   5495  Z= 0.278
  Chirality :  0.051   0.136    615
  Planarity :  0.003   0.029    705
  Dihedral  :  5.517  13.990    550
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.69 %
    Favored  : 85.81 %
  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: -2.44 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E 299 
 PHE   0.003   0.001   PHE A 378 
 TYR   0.006   0.003   TYR A 310 
 ARG   0.006   0.001   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
  112 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8492 (tt) cc_final: 0.8244 (mp)
REVERT: B  376 LEU cc_start: 0.8539 (tt) cc_final: 0.8248 (mp)
REVERT: B  379 ARG cc_start: 0.6816 (tpp-160) cc_final: 0.6231 (tpp80)
REVERT: C  376 LEU cc_start: 0.8693 (tm) cc_final: 0.8380 (mp)
  outliers start: 7
  outliers final: 0
  residues processed: 105
  average time/residue: 1.1394
  time to fit residues: 124.0943
Evaluate side-chains
  100 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0870
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    4.2166

-------------------------------------------------------------------------------
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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
C 336 GLN
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.126473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.114189 restraints weight = 4358.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.28
r_work: 0.3642 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4115  Z= 0.396
  Angle     :  0.628   5.062   5495  Z= 0.325
  Chirality :  0.052   0.146    615
  Planarity :  0.004   0.043    705
  Dihedral  :  5.871  14.934    550
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.84 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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   0.005   0.001   PHE E 346 
 TYR   0.008   0.003   TYR E 310 
 ARG   0.003   0.001   ARG B 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
  113 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  376 LEU cc_start: 0.8610 (tt) cc_final: 0.8285 (mp)
REVERT: D  319 THR cc_start: 0.8589 (m) cc_final: 0.8285 (p)
REVERT: D  376 LEU cc_start: 0.8525 (tt) cc_final: 0.8267 (mp)
REVERT: E  376 LEU cc_start: 0.8655 (tt) cc_final: 0.8374 (mp)
  outliers start: 7
  outliers final: 0
  residues processed: 107
  average time/residue: 1.0564
  time to fit residues: 117.1834
Evaluate side-chains
  103 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.1980
   chunk 35 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    3.0388

-------------------------------------------------------------------------------
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
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 GLN
E 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.128649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.116328 restraints weight = 4444.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.29
r_work: 0.3678 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4115  Z= 0.304
  Angle     :  0.589   7.047   5495  Z= 0.302
  Chirality :  0.052   0.148    615
  Planarity :  0.003   0.032    705
  Dihedral  :  5.749  14.623    550
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.27 %
    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: -2.44 (0.27), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (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   0.007   0.003   TYR E 310 
 ARG   0.003   0.001   ARG C 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
  110 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8618 (tm) cc_final: 0.8336 (mt)
REVERT: B  376 LEU cc_start: 0.8462 (tt) cc_final: 0.8189 (mp)
REVERT: C  376 LEU cc_start: 0.8667 (tm) cc_final: 0.8418 (mt)
REVERT: D  319 THR cc_start: 0.8580 (m) cc_final: 0.8281 (p)
REVERT: D  376 LEU cc_start: 0.8457 (tt) cc_final: 0.8219 (mp)
REVERT: E  376 LEU cc_start: 0.8578 (tt) cc_final: 0.8336 (mp)
  outliers start: 6
  outliers final: 0
  residues processed: 104
  average time/residue: 1.1203
  time to fit residues: 120.6265
Evaluate side-chains
  104 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 4 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 276 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.128731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.116410 restraints weight = 4310.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.29
r_work: 0.3679 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4115  Z= 0.283
  Angle     :  0.574   5.968   5495  Z= 0.296
  Chirality :  0.051   0.136    615
  Planarity :  0.003   0.032    705
  Dihedral  :  5.691  14.631    550
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.91 %
    Favored  : 81.94 %
  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: -2.41 (0.27), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (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   0.007   0.003   TYR E 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
  116 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.8616 (tm) cc_final: 0.8351 (mt)
REVERT: B  288 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7346 (mm110)
REVERT: B  376 LEU cc_start: 0.8459 (tt) cc_final: 0.8206 (mp)
REVERT: C  288 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7633 (mt0)
REVERT: C  376 LEU cc_start: 0.8640 (tm) cc_final: 0.8406 (mt)
REVERT: C  379 ARG cc_start: 0.4186 (OUTLIER) cc_final: 0.3359 (mpp-170)
REVERT: D  288 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7404 (mm110)
REVERT: D  376 LEU cc_start: 0.8458 (tt) cc_final: 0.8218 (mp)
REVERT: E  376 LEU cc_start: 0.8573 (tt) cc_final: 0.8346 (mp)
  outliers start: 10
  outliers final: 0
  residues processed: 107
  average time/residue: 1.1025
  time to fit residues: 122.3584
Evaluate side-chains
  108 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  288 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   overall best weight:    2.2984

-------------------------------------------------------------------------------
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 336 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.129364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.116526 restraints weight = 4368.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.31
r_work: 0.3679 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2411

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= 0.249
  Angle     :  0.557   5.686   5495  Z= 0.287
  Chirality :  0.051   0.135    615
  Planarity :  0.003   0.034    705
  Dihedral  :  5.607  14.475    550
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.99 %
    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: -2.39 (0.27), 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   0.000   HIS E 299 
 PHE   0.003   0.001   PHE B 346 
 TYR   0.007   0.003   TYR E 310 
 ARG   0.007   0.001   ARG A 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
  116 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: B  288 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7327 (mm110)
REVERT: C  288 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7667 (mt0)
REVERT: C  376 LEU cc_start: 0.8637 (tm) cc_final: 0.8402 (mt)
REVERT: C  379 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.4045 (mmm160)
REVERT: D  376 LEU cc_start: 0.8447 (tt) cc_final: 0.8185 (mp)
REVERT: E  376 LEU cc_start: 0.8550 (tt) cc_final: 0.8328 (mp)
  outliers start: 9
  outliers final: 0
  residues processed: 109
  average time/residue: 1.0761
  time to fit residues: 121.5831
Evaluate side-chains
  108 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  288 GLN
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    3.5188

-------------------------------------------------------------------------------
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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 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 = 0.3939 r_free = 0.3939 target = 0.128490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.115927 restraints weight = 4243.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.29
r_work: 0.3673 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4115  Z= 0.343
  Angle     :  0.612   5.122   5495  Z= 0.315
  Chirality :  0.053   0.144    615
  Planarity :  0.003   0.033    705
  Dihedral  :  5.834  14.831    550
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.77 %
    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: -2.39 (0.27), 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   0.015   0.001   PHE A 378 
 TYR   0.008   0.003   TYR E 310 
 ARG   0.002   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
  117 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: B  288 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7331 (mm110)
REVERT: C  277 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8359 (mm)
REVERT: C  288 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7649 (mt0)
REVERT: C  376 LEU cc_start: 0.8686 (tm) cc_final: 0.8459 (mt)
REVERT: C  379 ARG cc_start: 0.4631 (OUTLIER) cc_final: 0.4009 (mmm160)
REVERT: D  376 LEU cc_start: 0.8513 (tt) cc_final: 0.8279 (mp)
REVERT: E  376 LEU cc_start: 0.8585 (tt) cc_final: 0.8364 (mp)
  outliers start: 10
  outliers final: 1
  residues processed: 109
  average time/residue: 1.0787
  time to fit residues: 121.8381
Evaluate side-chains
  111 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 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 = 0.3939 r_free = 0.3939 target = 0.128307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.115752 restraints weight = 4255.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.29
r_work: 0.3673 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2535

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= 0.347
  Angle     :  0.644   9.864   5495  Z= 0.324
  Chirality :  0.054   0.222    615
  Planarity :  0.003   0.033    705
  Dihedral  :  5.866  14.852    550
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.42 %
    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: -2.37 (0.27), 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   0.015   0.001   PHE A 378 
 TYR   0.008   0.003   TYR E 310 
 ARG   0.002   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
  116 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: B  288 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7334 (mm110)
REVERT: C  277 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8370 (mm)
REVERT: C  288 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7648 (mt0)
REVERT: C  376 LEU cc_start: 0.8681 (tm) cc_final: 0.8463 (mt)
REVERT: C  379 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.3671 (mtm180)
REVERT: D  376 LEU cc_start: 0.8506 (tt) cc_final: 0.8287 (mp)
REVERT: E  376 LEU cc_start: 0.8602 (tt) cc_final: 0.8353 (mp)
  outliers start: 8
  outliers final: 1
  residues processed: 109
  average time/residue: 1.0766
  time to fit residues: 121.8447
Evaluate side-chains
  110 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   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**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 GLN
** C 336 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.128802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.116262 restraints weight = 4255.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 1.29
r_work: 0.3686 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2501

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= 0.322
  Angle     :  0.627   7.407   5495  Z= 0.316
  Chirality :  0.054   0.192    615
  Planarity :  0.003   0.032    705
  Dihedral  :  5.827  14.784    550
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.77
  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: -2.36 (0.27), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 299 
 PHE   0.014   0.001   PHE A 378 
 TYR   0.008   0.003   TYR E 310 
 ARG   0.002   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
  112 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 106
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  277 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8362 (mm)
REVERT: C  288 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7753 (mt0)
REVERT: C  376 LEU cc_start: 0.8681 (tm) cc_final: 0.8455 (mt)
REVERT: C  379 ARG cc_start: 0.4719 (OUTLIER) cc_final: 0.4118 (mtm180)
REVERT: D  376 LEU cc_start: 0.8467 (tt) cc_final: 0.8262 (mp)
REVERT: E  376 LEU cc_start: 0.8589 (tt) cc_final: 0.8350 (mp)
  outliers start: 6
  outliers final: 1
  residues processed: 107
  average time/residue: 1.1064
  time to fit residues: 122.6896
Evaluate side-chains
  110 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue  277 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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**
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 336 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 = 0.3956 r_free = 0.3956 target = 0.129191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.116664 restraints weight = 4271.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.29
r_work: 0.3687 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4115  Z= 0.314
  Angle     :  0.635  10.446   5495  Z= 0.316
  Chirality :  0.054   0.212    615
  Planarity :  0.003   0.032    705
  Dihedral  :  5.817  14.729    550
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.85 %
    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: -2.35 (0.27), 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   0.013   0.001   PHE A 378 
 TYR   0.007   0.003   TYR E 310 
 ARG   0.002   0.001   ARG C 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3776.31 seconds
wall clock time: 67 minutes 33.53 seconds (4053.53 seconds total)