Starting phenix.real_space_refine
on Sun Mar 10 18:59:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/03_2024/7p65_13218.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/03_2024/7p65_13218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/03_2024/7p65_13218.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/03_2024/7p65_13218.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/03_2024/7p65_13218.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p65_13218/03_2024/7p65_13218.pdb"
  }
  resolution = 2.7
  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    2575      2.51       5
     N     775      2.21       5
     O     785      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  348": "OD1" <-> "OD2"
    Residue "B ASP  348": "OD1" <-> "OD2"
    Residue "C ASP  348": "OD1" <-> "OD2"
    Residue "D ASP  348": "OD1" <-> "OD2"
    Residue "E ASP  348": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 4145
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "B"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "C"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "D"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "E"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
  Time building chain proxies: 2.57, per 1000 atoms: 0.62
  Number of scatterers: 4145
  At special positions: 0
  Unit cell: (67.85, 111.55, 46, 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     785      8.00
     N     775      7.00
     C    2575      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: 1.52
  Conformation dependent library (CDL) restraints added in 805.2 milliseconds
  

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  950

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 42.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 280
      removed outlier: 6.541A  pdb=" N   GLN B 276 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   ASN C 279 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ILE B 278 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLN A 276 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   ASN B 279 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ILE A 278 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 275 " --> pdb=" O   GLN D 276 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   ILE D 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE A 277 " --> pdb=" O   ILE D 278 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   LYS D 280 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASN A 279 " --> pdb=" O   LYS D 280 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 284 through 289
      removed outlier: 6.543A  pdb=" N   SER B 285 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   GLN C 288 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL B 287 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   SER A 285 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   GLN B 288 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 287 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 294 through 299
      removed outlier: 8.975A  pdb=" N   LYS B 294 " --> pdb=" O   ASP C 295 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   ILE C 297 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ASN B 296 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   HIS C 299 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LYS B 298 " --> pdb=" O   HIS C 299 " (cutoff:3.500A)
      removed outlier: 8.965A  pdb=" N   LYS A 294 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 8.946A  pdb=" N   ILE B 297 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ASN A 296 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   HIS B 299 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LYS A 298 " --> pdb=" O   HIS B 299 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ASP A 295 " --> pdb=" O   LYS D 294 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASN D 296 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP D 295 " --> pdb=" O   LYS E 294 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASN E 296 " --> pdb=" O   ASP D 295 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 307 through 310
      removed outlier: 6.562A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.842A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 320
      removed outlier: 6.557A  pdb=" N   LYS B 317 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   SER C 320 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   THR B 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   SER B 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   THR A 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 336 through 337
      removed outlier: 6.208A  pdb=" N   GLN A 336 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   GLN D 336 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 340 through 345
      removed outlier: 6.419A  pdb=" N   LYS B 340 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   LYS C 343 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU B 342 " --> pdb=" O   LYS C 343 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ASP C 345 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU B 344 " --> pdb=" O   ASP C 345 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LYS A 340 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS B 343 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLU A 342 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ASP B 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 354
      removed outlier: 6.345A  pdb=" N   ARG A 349 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   SER D 352 " --> pdb=" O   ARG A 349 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLN A 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   ILE D 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   LYS A 353 " --> pdb=" O   ILE D 354 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ARG D 349 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   SER E 352 " --> pdb=" O   ARG D 349 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   GLN D 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   ILE E 354 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LYS D 353 " --> pdb=" O   ILE E 354 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362
      removed outlier: 6.572A  pdb=" N   ASP A 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   THR D 361 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ILE A 360 " --> pdb=" O   THR D 361 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASP D 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   THR E 361 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ILE D 360 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 368 through 373
      removed outlier: 6.220A  pdb=" N   ASN A 368 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ILE D 371 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LYS A 370 " --> pdb=" O   ILE D 371 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   THR D 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLU A 372 " --> pdb=" O   THR D 373 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ASN D 368 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ILE E 371 " --> pdb=" O   ASN D 368 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LYS D 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   THR E 373 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLU D 372 " --> pdb=" O   THR E 373 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379
      removed outlier: 6.642A  pdb=" N   LEU B 376 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ARG C 379 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE B 378 " --> pdb=" O   ARG C 379 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ARG B 379 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   PHE A 378 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)

    85 hydrogen bonds defined for protein.
    255 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: 1.04

  Time building geometry restraints manager: 1.63 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: 1395
        1.34 -     1.46: 624
        1.46 -     1.57: 2171
        1.57 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 4200
  Sorted by residual:
  bond pdb=" N   LYS A 317 "
       pdb=" CA  LYS A 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.22e-02 6.72e+03 6.19e+00
  bond pdb=" N   ARG E 349 "
       pdb=" CA  ARG E 349 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.029 1.20e-02 6.94e+03 6.04e+00
  bond pdb=" N   LYS B 317 "
       pdb=" CA  LYS B 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.22e-02 6.72e+03 5.93e+00
  bond pdb=" N   LYS C 317 "
       pdb=" CA  LYS C 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.22e-02 6.72e+03 5.91e+00
  bond pdb=" N   LYS E 317 "
       pdb=" CA  LYS E 317 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.22e-02 6.72e+03 5.81e+00
  ... (remaining 4195 not shown)

  Histogram of bond angle deviations from ideal:
      101.90 -   107.76: 185
      107.76 -   113.63: 2382
      113.63 -   119.50: 1039
      119.50 -   125.37: 1959
      125.37 -   131.24: 45
  Bond angle restraints: 5610
  Sorted by residual:
  angle pdb=" CA  LEU B 315 "
        pdb=" CB  LEU B 315 "
        pdb=" CG  LEU B 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.97   -8.67 3.50e+00 8.16e-02 6.13e+00
  angle pdb=" CA  LEU A 315 "
        pdb=" CB  LEU A 315 "
        pdb=" CG  LEU A 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.96   -8.66 3.50e+00 8.16e-02 6.12e+00
  angle pdb=" CA  LEU E 315 "
        pdb=" CB  LEU E 315 "
        pdb=" CG  LEU E 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  angle pdb=" CA  LEU C 315 "
        pdb=" CB  LEU C 315 "
        pdb=" CG  LEU C 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  angle pdb=" CA  LEU D 315 "
        pdb=" CB  LEU D 315 "
        pdb=" CG  LEU D 315 "
      ideal   model   delta    sigma   weight residual
     116.30  124.95   -8.65 3.50e+00 8.16e-02 6.11e+00
  ... (remaining 5605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.96: 2229
       11.96 -    23.92: 216
       23.92 -    35.88: 100
       35.88 -    47.84: 21
       47.84 -    59.80: 14
  Dihedral angle restraints: 2580
    sinusoidal: 1080
      harmonic: 1500
  Sorted by residual:
  dihedral pdb=" CG  LYS D 331 "
           pdb=" CD  LYS D 331 "
           pdb=" CE  LYS D 331 "
           pdb=" NZ  LYS D 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.80  -59.80     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS A 331 "
           pdb=" CD  LYS A 331 "
           pdb=" CE  LYS A 331 "
           pdb=" NZ  LYS A 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.77  -59.77     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS C 331 "
           pdb=" CD  LYS C 331 "
           pdb=" CE  LYS C 331 "
           pdb=" NZ  LYS C 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.76  -59.76     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 310
       0.025 -    0.050: 167
       0.050 -    0.075: 38
       0.075 -    0.101: 64
       0.101 -    0.126: 46
  Chirality restraints: 625
  Sorted by residual:
  chirality pdb=" CA  LYS C 340 "
            pdb=" N   LYS C 340 "
            pdb=" C   LYS C 340 "
            pdb=" CB  LYS C 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  LYS D 340 "
            pdb=" N   LYS D 340 "
            pdb=" C   LYS D 340 "
            pdb=" CB  LYS D 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.63   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  ILE E 277 "
            pdb=" N   ILE E 277 "
            pdb=" C   ILE E 277 "
            pdb=" CB  ILE E 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 622 not shown)

  Planarity restraints: 725
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 300 "    0.016 5.00e-02 4.00e+02   2.46e-02 9.69e-01
        pdb=" N   PRO C 301 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO C 301 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 301 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 300 "    0.016 5.00e-02 4.00e+02   2.45e-02 9.61e-01
        pdb=" N   PRO E 301 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO E 301 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 301 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 300 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.48e-01
        pdb=" N   PRO A 301 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 301 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 301 "    0.013 5.00e-02 4.00e+02
  ... (remaining 722 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 1459
        2.88 -     3.39: 3289
        3.39 -     3.89: 7295
        3.89 -     4.40: 7622
        4.40 -     4.90: 15606
  Nonbonded interactions: 35271
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 346 "
            pdb=" NZ  LYS B 311 "
     model   vdw
     2.381 2.520
  nonbonded pdb=" O   PHE B 346 "
            pdb=" NZ  LYS C 311 "
     model   vdw
     2.398 2.520
  nonbonded pdb=" NZ  LYS A 311 "
            pdb=" O   PHE D 346 "
     model   vdw
     2.398 2.520
  nonbonded pdb=" NZ  LYS D 311 "
            pdb=" O   PHE E 346 "
     model   vdw
     2.404 2.520
  nonbonded pdb=" ND1 HIS E 299 "
            pdb=" OH  TYR E 310 "
     model   vdw
     2.475 2.520
  ... (remaining 35266 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:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          8.000
  Check model and map are aligned:         0.060
  Set scattering table:                    0.030
  Process input model:                     15.500
  Find NCS groups from input model:        0.260
  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:16.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
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   0.055   4200  Z= 0.263
  Angle     :  0.627   8.666   5610  Z= 0.319
  Chirality :  0.050   0.126    625
  Planarity :  0.003   0.025    725
  Dihedral  : 12.602  59.802   1630
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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: -2.90 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 299 
 PHE   0.004   0.001   PHE A 378 
 TYR   0.004   0.001   TYR B 310 
 ARG   0.002   0.001   ARG B 349 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.518 
Fit side-chains
REVERT: C  316 SER cc_start: 0.8478 (p) cc_final: 0.8222 (m)
REVERT: D  307 GLN cc_start: 0.8115 (mt0) cc_final: 0.7860 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 1.0295
  time to fit residues: 136.7482
Evaluate side-chains
  99 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 276 GLN
C 296 ASN
C 359 ASN
C 381 ASN
D 296 ASN
D 359 ASN
D 368 ASN
D 381 ASN
E 359 ASN
E 381 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   4200  Z= 0.372
  Angle     :  0.619   9.703   5610  Z= 0.289
  Chirality :  0.049   0.146    625
  Planarity :  0.002   0.015    725
  Dihedral  :  4.212  12.175    560
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.42 %
    Favored  : 86.53 %
  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: -2.75 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 299 
 PHE   0.011   0.002   PHE D 378 
 TYR   0.013   0.002   TYR D 310 
 ARG   0.002   0.001   ARG E 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.547 
Fit side-chains
REVERT: C  316 SER cc_start: 0.8758 (p) cc_final: 0.8516 (m)
  outliers start: 5
  outliers final: 3
  residues processed: 103
  average time/residue: 0.7836
  time to fit residues: 84.5648
Evaluate side-chains
  97 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue  276 GLN
Chi-restraints excluded: chain E residue  316 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 50 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   overall best weight:    3.0786

-------------------------------------------------------------------------------
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 381 ASN
B 276 GLN
B 296 ASN
B 381 ASN
C 359 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   4200  Z= 0.432
  Angle     :  0.638   9.271   5610  Z= 0.299
  Chirality :  0.049   0.157    625
  Planarity :  0.002   0.013    725
  Dihedral  :  4.304  12.804    560
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 16.42 %
    Favored  : 82.95 %
  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: -2.81 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 PHE   0.012   0.002   PHE D 378 
 TYR   0.011   0.002   TYR D 310 
 ARG   0.002   0.001   ARG C 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.533 
Fit side-chains
REVERT: C  316 SER cc_start: 0.8896 (p) cc_final: 0.8612 (m)
  outliers start: 3
  outliers final: 3
  residues processed: 102
  average time/residue: 0.8350
  time to fit residues: 89.2835
Evaluate side-chains
  101 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  356 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 381 ASN
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 296 ASN
B 359 ASN
B 381 ASN
C 296 ASN
C 381 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4200  Z= 0.228
  Angle     :  0.564   8.353   5610  Z= 0.262
  Chirality :  0.048   0.122    625
  Planarity :  0.002   0.010    725
  Dihedral  :  4.134  12.034    560
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 17.68 %
    Favored  : 81.05 %
  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: -2.79 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 299 
 PHE   0.008   0.001   PHE D 378 
 TYR   0.010   0.002   TYR D 310 
 ARG   0.001   0.000   ARG C 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.520 
Fit side-chains
REVERT: C  316 SER cc_start: 0.8877 (p) cc_final: 0.8562 (m)
REVERT: D  348 ASP cc_start: 0.7529 (m-30) cc_final: 0.7174 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 103
  average time/residue: 0.8642
  time to fit residues: 93.2470
Evaluate side-chains
  99 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain D residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0770
   chunk 45 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    2.3944

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 381 ASN
D 276 GLN
D 381 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4200  Z= 0.347
  Angle     :  0.578   8.660   5610  Z= 0.275
  Chirality :  0.048   0.121    625
  Planarity :  0.002   0.011    725
  Dihedral  :  4.210  12.728    560
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.11 %
    Favored  : 79.37 %
  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: -2.82 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 299 
 PHE   0.010   0.002   PHE D 378 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.001   0.000   ARG B 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.521 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.7441 (m-30) cc_final: 0.7217 (m-30)
  outliers start: 12
  outliers final: 5
  residues processed: 102
  average time/residue: 0.8664
  time to fit residues: 92.5071
Evaluate side-chains
  101 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 31 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4200  Z= 0.276
  Angle     :  0.575   7.996   5610  Z= 0.270
  Chirality :  0.049   0.155    625
  Planarity :  0.002   0.012    725
  Dihedral  :  4.156  12.464    560
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.37 %
    Favored  : 78.53 %
  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: -2.82 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 299 
 PHE   0.009   0.001   PHE D 378 
 TYR   0.010   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.518 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.7454 (m-30) cc_final: 0.7224 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 103
  average time/residue: 0.8133
  time to fit residues: 87.9548
Evaluate side-chains
  104 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 296 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4200  Z= 0.216
  Angle     :  0.567   9.072   5610  Z= 0.265
  Chirality :  0.048   0.121    625
  Planarity :  0.002   0.010    725
  Dihedral  :  4.061  12.032    560
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.00 %
    Favored  : 78.32 %
  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: -2.78 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 299 
 PHE   0.008   0.001   PHE D 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.542 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.7446 (m-30) cc_final: 0.7204 (m-30)
  outliers start: 8
  outliers final: 4
  residues processed: 98
  average time/residue: 0.8166
  time to fit residues: 84.1075
Evaluate side-chains
  98 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 381 ASN
D 276 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4200  Z= 0.196
  Angle     :  0.573   7.586   5610  Z= 0.265
  Chirality :  0.049   0.119    625
  Planarity :  0.002   0.010    725
  Dihedral  :  3.989  11.843    560
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.63 %
    Favored  : 77.47 %
  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: -2.77 (0.30), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 299 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.001   0.000   ARG C 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8394 (tt)
REVERT: B  348 ASP cc_start: 0.7448 (m-30) cc_final: 0.7204 (m-30)
  outliers start: 9
  outliers final: 5
  residues processed: 100
  average time/residue: 0.8626
  time to fit residues: 90.5803
Evaluate side-chains
  99 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  300 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 44 optimal weight:    0.1980
   chunk 46 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 296 ASN
B 307 GLN
B 359 ASN
B 381 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4200  Z= 0.179
  Angle     :  0.567   7.382   5610  Z= 0.263
  Chirality :  0.049   0.119    625
  Planarity :  0.002   0.009    725
  Dihedral  :  3.932  11.686    560
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 21.05 %
    Favored  : 77.47 %
  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: -2.73 (0.30), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 299 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.009   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8436 (tt)
REVERT: B  348 ASP cc_start: 0.7403 (m-30) cc_final: 0.7165 (m-30)
  outliers start: 7
  outliers final: 3
  residues processed: 102
  average time/residue: 0.7806
  time to fit residues: 83.6643
Evaluate side-chains
  97 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain E residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 46 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
B 276 GLN
B 296 ASN
B 359 ASN
B 381 ASN
C 296 ASN
C 381 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4200  Z= 0.221
  Angle     :  0.585   8.860   5610  Z= 0.271
  Chirality :  0.049   0.118    625
  Planarity :  0.002   0.010    725
  Dihedral  :  3.971  12.079    560
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 21.05 %
    Favored  : 77.89 %
  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: -2.75 (0.30), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 299 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.010   0.002   TYR D 310 
 ARG   0.001   0.000   ARG D 379 

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

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

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1080 Ramachandran restraints generated.
    540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8443 (tt)
REVERT: B  348 ASP cc_start: 0.7388 (m-30) cc_final: 0.7149 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 97
  average time/residue: 0.8266
  time to fit residues: 84.1890
Evaluate side-chains
  97 residues out of total 475 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  379 ARG
Chi-restraints excluded: chain D residue  300 VAL
Chi-restraints excluded: chain E residue  300 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 381 ASN
B 296 ASN
B 381 ASN
C 381 ASN
D 381 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.090713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.077339 restraints weight = 5553.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.11
r_work: 0.3103 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.042   4200  Z= 0.521
  Angle     :  0.686   8.640   5610  Z= 0.327
  Chirality :  0.050   0.122    625
  Planarity :  0.002   0.015    725
  Dihedral  :  4.325  14.501    560
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 21.26 %
    Favored  : 77.68 %
  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: -2.90 (0.29), residues: 540
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.22), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 299 
 PHE   0.011   0.002   PHE D 378 
 TYR   0.015   0.003   TYR E 310 
 ARG   0.002   0.001   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2108.84 seconds
wall clock time: 38 minutes 24.72 seconds (2304.72 seconds total)