Starting phenix.real_space_refine
on Sun Jul 27 19:16:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xye_10649/07_2025/6xye_10649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xye_10649/07_2025/6xye_10649.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xye_10649/07_2025/6xye_10649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xye_10649/07_2025/6xye_10649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xye_10649/07_2025/6xye_10649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xye_10649/07_2025/6xye_10649.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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      57      5.16       5
     C    6219      2.51       5
     N    1656      2.21       5
     O    1902      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9834
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 588
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "B"
      Number of atoms: 2690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2690
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 13, 'TRANS': 343}
  Restraints were copied for chains:
    D, F, C, E
  Time building chain proxies: 5.29, per 1000 atoms: 0.54
  Number of scatterers: 9834
  At special positions: 0
  Unit cell: (102.1, 106.184, 101.079, 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      57     16.00
     O    1902      8.00
     N    1656      7.00
     C    6219      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS B 307 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 446 " - pdb=" SG  CYS B 455 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 470 " - pdb=" SG  CYS B 478 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 502 " - pdb=" SG  CYS B 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 509 " - pdb=" SG  CYS B 532 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 180 " - pdb=" SG  CYS D 307 " distance=2.06
    Simple disulfide: pdb=" SG  CYS E 180 " - pdb=" SG  CYS F 307 " distance=2.06
    Simple disulfide: pdb=" SG  CYS D 446 " - pdb=" SG  CYS D 455 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 446 " - pdb=" SG  CYS F 455 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 470 " - pdb=" SG  CYS D 478 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 470 " - pdb=" SG  CYS F 478 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 502 " - pdb=" SG  CYS D 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 502 " - pdb=" SG  CYS F 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 509 " - pdb=" SG  CYS D 532 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 509 " - pdb=" SG  CYS F 532 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2400

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 24 sheets defined
      29.2% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 139 through 142
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 182 through 207
      removed outlier: 3.689A  pdb=" N   LYS A 190 " --> pdb=" O   GLY A 186 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
      Proline residue:  A 198  - end of helix
    Processing helix  chain 'B' and resid 232 through 235
      No H-bonds generated for 'chain 'B' and resid 232 through 235'
    Processing helix  chain 'B' and resid 240 through 251
    Processing helix  chain 'B' and resid 260 through 268
      removed outlier: 3.670A  pdb=" N   GLU B 267 " --> pdb=" O   ARG B 263 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   GLN B 268 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 307 through 328
    Processing helix  chain 'B' and resid 355 through 360
    Processing helix  chain 'B' and resid 368 through 372
    Processing helix  chain 'B' and resid 465 through 473
      removed outlier: 5.344A  pdb=" N   CYS B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG B 472 " --> pdb=" O   GLN B 468 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY B 473 " --> pdb=" O   GLN B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 582
    Processing helix  chain 'C' and resid 139 through 142
    Processing helix  chain 'C' and resid 175 through 177
      No H-bonds generated for 'chain 'C' and resid 175 through 177'
    Processing helix  chain 'C' and resid 182 through 207
      removed outlier: 3.690A  pdb=" N   LYS C 190 " --> pdb=" O   GLY C 186 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN C 193 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER C 194 " --> pdb=" O   LYS C 190 " (cutoff:3.500A)
      Proline residue:  C 198  - end of helix
    Processing helix  chain 'D' and resid 232 through 235
      No H-bonds generated for 'chain 'D' and resid 232 through 235'
    Processing helix  chain 'D' and resid 240 through 251
    Processing helix  chain 'D' and resid 260 through 268
      removed outlier: 3.670A  pdb=" N   GLU D 267 " --> pdb=" O   ARG D 263 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   GLN D 268 " --> pdb=" O   THR D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 296
    Processing helix  chain 'D' and resid 300 through 304
    Processing helix  chain 'D' and resid 307 through 328
    Processing helix  chain 'D' and resid 355 through 360
    Processing helix  chain 'D' and resid 368 through 372
    Processing helix  chain 'D' and resid 465 through 473
      removed outlier: 5.344A  pdb=" N   CYS D 470 " --> pdb=" O   LEU D 466 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE D 471 " --> pdb=" O   LEU D 467 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG D 472 " --> pdb=" O   GLN D 468 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY D 473 " --> pdb=" O   GLN D 469 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 568 through 582
    Processing helix  chain 'E' and resid 139 through 142
    Processing helix  chain 'E' and resid 175 through 177
      No H-bonds generated for 'chain 'E' and resid 175 through 177'
    Processing helix  chain 'E' and resid 182 through 207
      removed outlier: 3.689A  pdb=" N   LYS E 190 " --> pdb=" O   GLY E 186 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN E 193 " --> pdb=" O   GLU E 189 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER E 194 " --> pdb=" O   LYS E 190 " (cutoff:3.500A)
      Proline residue:  E 198  - end of helix
    Processing helix  chain 'F' and resid 232 through 235
      No H-bonds generated for 'chain 'F' and resid 232 through 235'
    Processing helix  chain 'F' and resid 240 through 251
    Processing helix  chain 'F' and resid 260 through 268
      removed outlier: 3.670A  pdb=" N   GLU F 267 " --> pdb=" O   ARG F 263 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLN F 268 " --> pdb=" O   THR F 264 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 291 through 296
    Processing helix  chain 'F' and resid 300 through 304
    Processing helix  chain 'F' and resid 307 through 328
    Processing helix  chain 'F' and resid 355 through 360
    Processing helix  chain 'F' and resid 368 through 372
    Processing helix  chain 'F' and resid 465 through 473
      removed outlier: 5.343A  pdb=" N   CYS F 470 " --> pdb=" O   LEU F 466 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE F 471 " --> pdb=" O   LEU F 467 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG F 472 " --> pdb=" O   GLN F 468 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY F 473 " --> pdb=" O   GLN F 469 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 568 through 582
    Processing sheet with id=A, first strand: chain 'B' and resid 446 through 448
      removed outlier: 7.862A  pdb=" N   ALA B 453 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   HIS A 154 " --> pdb=" O   ALA B 453 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   CYS B 455 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LYS A 156 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ASP A 151 " --> pdb=" O   ARG B 410 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 155 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   VAL B 406 " --> pdb=" O   TYR A 155 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 156 through 159
    Processing sheet with id=C, first strand: chain 'A' and resid 163 through 169
      removed outlier: 6.275A  pdb=" N   SER B 394 " --> pdb=" O   ILE B 381 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE B 381 " --> pdb=" O   SER B 394 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   SER B 396 " --> pdb=" O   THR B 379 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   THR B 379 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'B' and resid 273 through 276
      removed outlier: 6.190A  pdb=" N   ILE B 273 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL B 287 " --> pdb=" O   ILE B 273 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU B 275 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B 285 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=D
    Processing sheet with id=E, first strand: chain 'B' and resid 416 through 418
    Processing sheet with id=F, first strand: chain 'B' and resid 424 through 425
    Processing sheet with id=G, first strand: chain 'B' and resid 491 through 494
    Processing sheet with id=H, first strand: chain 'B' and resid 507 through 509
    Processing sheet with id=I, first strand: chain 'D' and resid 446 through 448
      removed outlier: 7.861A  pdb=" N   ALA D 453 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   HIS C 154 " --> pdb=" O   ALA D 453 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   CYS D 455 " --> pdb=" O   HIS C 154 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LYS C 156 " --> pdb=" O   CYS D 455 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP C 151 " --> pdb=" O   ARG D 410 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR C 155 " --> pdb=" O   VAL D 406 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   VAL D 406 " --> pdb=" O   TYR C 155 " (cutoff:3.500A)
    Processing sheet with id=J, first strand: chain 'C' and resid 156 through 159
    Processing sheet with id=K, first strand: chain 'C' and resid 163 through 169
      removed outlier: 6.275A  pdb=" N   SER D 394 " --> pdb=" O   ILE D 381 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE D 381 " --> pdb=" O   SER D 394 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   SER D 396 " --> pdb=" O   THR D 379 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   THR D 379 " --> pdb=" O   SER D 396 " (cutoff:3.500A)
    Processing sheet with id=L, first strand: chain 'D' and resid 273 through 276
      removed outlier: 6.190A  pdb=" N   ILE D 273 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL D 287 " --> pdb=" O   ILE D 273 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU D 275 " --> pdb=" O   ILE D 285 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE D 285 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=L
    Processing sheet with id=M, first strand: chain 'D' and resid 416 through 418
    Processing sheet with id=N, first strand: chain 'D' and resid 424 through 425
    Processing sheet with id=O, first strand: chain 'D' and resid 491 through 494
    Processing sheet with id=P, first strand: chain 'D' and resid 507 through 509
    Processing sheet with id=Q, first strand: chain 'F' and resid 446 through 448
      removed outlier: 7.862A  pdb=" N   ALA F 453 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   HIS E 154 " --> pdb=" O   ALA F 453 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   CYS F 455 " --> pdb=" O   HIS E 154 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LYS E 156 " --> pdb=" O   CYS F 455 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ASP E 151 " --> pdb=" O   ARG F 410 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR E 155 " --> pdb=" O   VAL F 406 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   VAL F 406 " --> pdb=" O   TYR E 155 " (cutoff:3.500A)
    Processing sheet with id=R, first strand: chain 'E' and resid 156 through 159
    Processing sheet with id=S, first strand: chain 'E' and resid 163 through 169
      removed outlier: 6.276A  pdb=" N   SER F 394 " --> pdb=" O   ILE F 381 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE F 381 " --> pdb=" O   SER F 394 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   SER F 396 " --> pdb=" O   THR F 379 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   THR F 379 " --> pdb=" O   SER F 396 " (cutoff:3.500A)
    Processing sheet with id=T, first strand: chain 'F' and resid 273 through 276
      removed outlier: 6.190A  pdb=" N   ILE F 273 " --> pdb=" O   VAL F 287 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL F 287 " --> pdb=" O   ILE F 273 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU F 275 " --> pdb=" O   ILE F 285 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE F 285 " --> pdb=" O   GLU F 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=T
    Processing sheet with id=U, first strand: chain 'F' and resid 416 through 418
    Processing sheet with id=V, first strand: chain 'F' and resid 424 through 425
    Processing sheet with id=W, first strand: chain 'F' and resid 491 through 494
    Processing sheet with id=X, first strand: chain 'F' and resid 507 through 509

    330 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2890
        1.34 -     1.46: 1651
        1.46 -     1.58: 5353
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 9978
  Sorted by residual:
  bond pdb=" N   VAL B 427 "
       pdb=" CA  VAL B 427 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 9.10e-03 1.21e+04 1.21e+01
  bond pdb=" N   VAL F 427 "
       pdb=" CA  VAL F 427 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.031 9.10e-03 1.21e+04 1.17e+01
  bond pdb=" N   VAL D 427 "
       pdb=" CA  VAL D 427 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.031 9.10e-03 1.21e+04 1.16e+01
  bond pdb=" CA  SER B 459 "
       pdb=" CB  SER B 459 "
    ideal  model  delta    sigma   weight residual
    1.537  1.492  0.045 1.38e-02 5.25e+03 1.06e+01
  bond pdb=" CA  SER D 459 "
       pdb=" CB  SER D 459 "
    ideal  model  delta    sigma   weight residual
    1.537  1.492  0.045 1.38e-02 5.25e+03 1.05e+01
  ... (remaining 9973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 10914
        1.55 -     3.11: 2204
        3.11 -     4.66: 356
        4.66 -     6.21: 53
        6.21 -     7.77: 21
  Bond angle restraints: 13548
  Sorted by residual:
  angle pdb=" N   GLY B 365 "
        pdb=" CA  GLY B 365 "
        pdb=" C   GLY B 365 "
      ideal   model   delta    sigma   weight residual
     115.36  109.42    5.94 1.33e+00 5.65e-01 1.99e+01
  angle pdb=" N   GLY D 365 "
        pdb=" CA  GLY D 365 "
        pdb=" C   GLY D 365 "
      ideal   model   delta    sigma   weight residual
     115.36  109.42    5.94 1.33e+00 5.65e-01 1.99e+01
  angle pdb=" N   GLY F 365 "
        pdb=" CA  GLY F 365 "
        pdb=" C   GLY F 365 "
      ideal   model   delta    sigma   weight residual
     115.36  109.45    5.91 1.33e+00 5.65e-01 1.98e+01
  angle pdb=" CA  GLY F 561 "
        pdb=" C   GLY F 561 "
        pdb=" O   GLY F 561 "
      ideal   model   delta    sigma   weight residual
     122.46  118.49    3.97 9.70e-01 1.06e+00 1.68e+01
  angle pdb=" CA  GLY B 561 "
        pdb=" C   GLY B 561 "
        pdb=" O   GLY B 561 "
      ideal   model   delta    sigma   weight residual
     122.46  118.55    3.91 9.70e-01 1.06e+00 1.62e+01
  ... (remaining 13543 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 5653
       14.85 -    29.69: 426
       29.69 -    44.53: 47
       44.53 -    59.38: 3
       59.38 -    74.22: 3
  Dihedral angle restraints: 6132
    sinusoidal: 2394
      harmonic: 3738
  Sorted by residual:
  dihedral pdb=" CA  ILE F 418 "
           pdb=" C   ILE F 418 "
           pdb=" N   GLY F 419 "
           pdb=" CA  GLY F 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.29  -29.71     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  ILE D 418 "
           pdb=" C   ILE D 418 "
           pdb=" N   GLY D 419 "
           pdb=" CA  GLY D 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.29  -29.71     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  ILE B 418 "
           pdb=" C   ILE B 418 "
           pdb=" N   GLY B 419 "
           pdb=" CA  GLY B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.31  -29.69     0      5.00e+00 4.00e-02 3.53e+01
  ... (remaining 6129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 891
       0.058 -    0.115: 467
       0.115 -    0.173: 173
       0.173 -    0.231: 107
       0.231 -    0.288: 9
  Chirality restraints: 1647
  Sorted by residual:
  chirality pdb=" CA  TYR F 397 "
            pdb=" N   TYR F 397 "
            pdb=" C   TYR F 397 "
            pdb=" CB  TYR F 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  TYR D 397 "
            pdb=" N   TYR D 397 "
            pdb=" C   TYR D 397 "
            pdb=" CB  TYR D 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  TYR B 397 "
            pdb=" N   TYR B 397 "
            pdb=" C   TYR B 397 "
            pdb=" CB  TYR B 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.06e+00
  ... (remaining 1644 not shown)

  Planarity restraints: 1716
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET F 302 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   MET F 302 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   MET F 302 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLN F 303 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 302 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   MET B 302 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   MET B 302 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLN B 303 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET D 302 "    0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   MET D 302 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   MET D 302 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLN D 303 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1713 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2897
        2.83 -     3.35: 9343
        3.35 -     3.87: 15826
        3.87 -     4.38: 17131
        4.38 -     4.90: 28703
  Nonbonded interactions: 73900
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F 382 "
            pdb=" O   ILE F 392 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG1 THR D 382 "
            pdb=" O   ILE D 392 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG1 THR B 382 "
            pdb=" O   ILE B 392 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   GLN B 543 "
            pdb=" N   GLY F 232 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" OH  TYR F 321 "
            pdb=" O   ALA F 349 "
     model   vdw
     2.366 3.040
  ... (remaining 73895 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     23.840
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
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      :  0.010   0.051   9993  Z= 0.662
  Angle     :  1.584  54.050  13578  Z= 1.009
  Chirality :  0.087   0.288   1647
  Planarity :  0.007   0.042   1716
  Dihedral  : 10.029  74.225   3687
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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: -3.09 (0.21), residues: 1281
  helix: -1.87 (0.25), residues: 342
  sheet: -3.21 (0.41), residues: 105
  loop : -2.05 (0.20), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.006   TRP E 139 
 HIS   0.012   0.002   HIS F 409 
 PHE   0.016   0.003   PHE F 448 
 TYR   0.027   0.004   TYR B 293 
 ARG   0.005   0.001   ARG F 480 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18404 (  330)
  hydrogen bonds       : angle       7.56514 (  891)
  SS BOND              : bond        0.01536 (   15)
  SS BOND              : angle      19.44644 (   30)
  covalent geometry    : bond        0.00992 ( 9978)
  covalent geometry    : angle       1.29462 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 380
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8999 (mt) cc_final: 0.8697 (mt)
REVERT: A  173 ASN cc_start: 0.7386 (t0) cc_final: 0.7112 (t0)
REVERT: A  193 ASN cc_start: 0.8737 (m-40) cc_final: 0.8248 (m-40)
REVERT: B  322 TYR cc_start: 0.7309 (t80) cc_final: 0.5901 (t80)
REVERT: B  385 ASP cc_start: 0.6926 (t70) cc_final: 0.6679 (m-30)
REVERT: B  389 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7389 (mptt)
REVERT: B  411 LEU cc_start: 0.8406 (mt) cc_final: 0.8122 (mp)
REVERT: B  412 GLU cc_start: 0.8062 (tp30) cc_final: 0.7503 (tp30)
REVERT: B  460 LEU cc_start: 0.9090 (mt) cc_final: 0.8781 (tt)
REVERT: B  463 MET cc_start: 0.6900 (ttm) cc_final: 0.5346 (ttm)
REVERT: C  142 LEU cc_start: 0.9009 (mt) cc_final: 0.8708 (mt)
REVERT: C  173 ASN cc_start: 0.7560 (t0) cc_final: 0.7325 (t0)
REVERT: C  193 ASN cc_start: 0.8798 (m-40) cc_final: 0.8162 (m-40)
REVERT: D  389 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7525 (mptt)
REVERT: D  436 TYR cc_start: 0.6971 (t80) cc_final: 0.6659 (t80)
REVERT: D  463 MET cc_start: 0.6952 (ttm) cc_final: 0.5710 (ttm)
REVERT: D  551 ASP cc_start: 0.7378 (m-30) cc_final: 0.6743 (t70)
REVERT: D  580 LYS cc_start: 0.9178 (tttt) cc_final: 0.8485 (mttm)
REVERT: E  142 LEU cc_start: 0.9012 (mt) cc_final: 0.8709 (mt)
REVERT: E  173 ASN cc_start: 0.7548 (t0) cc_final: 0.7313 (t0)
REVERT: E  193 ASN cc_start: 0.8685 (m-40) cc_final: 0.8469 (m-40)
REVERT: F  276 ILE cc_start: 0.8922 (mm) cc_final: 0.8709 (pt)
REVERT: F  302 MET cc_start: 0.7249 (mmm) cc_final: 0.6951 (mmt)
REVERT: F  389 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7583 (mptt)
REVERT: F  422 GLU cc_start: 0.6669 (tt0) cc_final: 0.6319 (mp0)
REVERT: F  430 TYR cc_start: 0.8339 (m-80) cc_final: 0.8056 (m-80)
REVERT: F  436 TYR cc_start: 0.7039 (t80) cc_final: 0.6799 (t80)
REVERT: F  463 MET cc_start: 0.6671 (ttm) cc_final: 0.5420 (ttm)
REVERT: F  510 TYR cc_start: 0.7011 (t80) cc_final: 0.6364 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 380
  average time/residue: 0.2342
  time to fit residues: 120.3502
Evaluate side-chains
  251 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0270
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 98 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0770
   chunk 60 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 114 optimal weight:    7.9990
   overall best weight:    1.3600

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
B 295 ASN
B 296 ASN
B 304 HIS
C 138 HIS
C 209 ASN
D 295 ASN
D 296 ASN
D 304 HIS
D 497 ASN
D 518 GLN
E 138 HIS
E 209 ASN
F 260 GLN
F 295 ASN
F 296 ASN
F 304 HIS
F 497 ASN
F 518 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.164836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.142165 restraints weight = 19444.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.145790 restraints weight = 12820.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.148366 restraints weight = 9326.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9993  Z= 0.139
  Angle     :  0.681   7.792  13578  Z= 0.358
  Chirality :  0.047   0.330   1647
  Planarity :  0.004   0.035   1716
  Dihedral  :  6.436  36.307   1377
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.13 (0.22), residues: 1281
  helix: -0.53 (0.26), residues: 360
  sheet: -2.59 (0.43), residues: 105
  loop : -1.73 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 423 
 HIS   0.003   0.001   HIS D 250 
 PHE   0.010   0.002   PHE D 329 
 TYR   0.016   0.001   TYR D 424 
 ARG   0.005   0.001   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05143 (  330)
  hydrogen bonds       : angle       5.63863 (  891)
  SS BOND              : bond        0.00758 (   15)
  SS BOND              : angle       2.49506 (   30)
  covalent geometry    : bond        0.00300 ( 9978)
  covalent geometry    : angle       0.67145 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8856 (mt) cc_final: 0.8578 (mt)
REVERT: A  147 ILE cc_start: 0.8458 (mm) cc_final: 0.8215 (mm)
REVERT: A  193 ASN cc_start: 0.8890 (m-40) cc_final: 0.8424 (m-40)
REVERT: B  293 TYR cc_start: 0.5202 (t80) cc_final: 0.4913 (t80)
REVERT: B  322 TYR cc_start: 0.7284 (t80) cc_final: 0.6040 (t80)
REVERT: B  385 ASP cc_start: 0.6727 (t70) cc_final: 0.6425 (m-30)
REVERT: B  389 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7261 (mptt)
REVERT: B  408 VAL cc_start: 0.8399 (t) cc_final: 0.8168 (t)
REVERT: B  411 LEU cc_start: 0.8388 (mt) cc_final: 0.8171 (mp)
REVERT: B  412 GLU cc_start: 0.8260 (tp30) cc_final: 0.7545 (tp30)
REVERT: B  463 MET cc_start: 0.6591 (ttm) cc_final: 0.6358 (ttm)
REVERT: B  487 MET cc_start: 0.5594 (tmm) cc_final: 0.5389 (tmm)
REVERT: B  551 ASP cc_start: 0.7320 (m-30) cc_final: 0.6769 (t70)
REVERT: C  142 LEU cc_start: 0.8813 (mt) cc_final: 0.8599 (mt)
REVERT: C  147 ILE cc_start: 0.8299 (mm) cc_final: 0.7995 (mm)
REVERT: C  176 LEU cc_start: 0.7773 (mt) cc_final: 0.7170 (tt)
REVERT: C  193 ASN cc_start: 0.8937 (m-40) cc_final: 0.8400 (m-40)
REVERT: D  275 GLU cc_start: 0.7174 (pt0) cc_final: 0.6764 (pm20)
REVERT: D  389 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7451 (mptt)
REVERT: D  436 TYR cc_start: 0.7409 (t80) cc_final: 0.6998 (t80)
REVERT: D  551 ASP cc_start: 0.7164 (m-30) cc_final: 0.6635 (t70)
REVERT: E  142 LEU cc_start: 0.8763 (mt) cc_final: 0.8523 (mt)
REVERT: E  147 ILE cc_start: 0.8486 (mm) cc_final: 0.8239 (mm)
REVERT: F  275 GLU cc_start: 0.7050 (pt0) cc_final: 0.6841 (pm20)
REVERT: F  302 MET cc_start: 0.7357 (mmm) cc_final: 0.7069 (mmt)
REVERT: F  312 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7728 (tp-100)
REVERT: F  314 LEU cc_start: 0.9225 (mt) cc_final: 0.9014 (mt)
REVERT: F  322 TYR cc_start: 0.7500 (t80) cc_final: 0.7290 (t80)
REVERT: F  385 ASP cc_start: 0.8041 (m-30) cc_final: 0.7678 (m-30)
REVERT: F  389 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7593 (mptt)
REVERT: F  430 TYR cc_start: 0.8291 (m-80) cc_final: 0.7678 (m-80)
REVERT: F  487 MET cc_start: 0.5550 (tmm) cc_final: 0.5329 (tmm)
REVERT: F  508 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7721 (mtmm)
REVERT: F  510 TYR cc_start: 0.6803 (t80) cc_final: 0.6347 (t80)
REVERT: F  551 ASP cc_start: 0.7577 (m-30) cc_final: 0.6312 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 305
  average time/residue: 0.2015
  time to fit residues: 86.0791
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 35 optimal weight:   20.0000
   chunk 4 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0970
   chunk 91 optimal weight:    0.0020
   chunk 114 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.4590

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

Flipped N/Q/H residues before XYZ refinement:
B 312 GLN
B 497 ASN
B 518 GLN
C 138 HIS
D 312 GLN
D 383 HIS
E 138 HIS
F 296 ASN
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.164427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.142176 restraints weight = 19818.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.145660 restraints weight = 13050.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.148165 restraints weight = 9461.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9993  Z= 0.125
  Angle     :  0.616   6.569  13578  Z= 0.328
  Chirality :  0.046   0.219   1647
  Planarity :  0.004   0.040   1716
  Dihedral  :  5.940  27.539   1377
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.23), residues: 1281
  helix: -0.09 (0.27), residues: 360
  sheet: -2.01 (0.43), residues: 117
  loop : -1.79 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 423 
 HIS   0.003   0.001   HIS D 250 
 PHE   0.008   0.002   PHE D 526 
 TYR   0.014   0.001   TYR D 424 
 ARG   0.007   0.001   ARG D 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04604 (  330)
  hydrogen bonds       : angle       5.29629 (  891)
  SS BOND              : bond        0.00389 (   15)
  SS BOND              : angle       1.33733 (   30)
  covalent geometry    : bond        0.00268 ( 9978)
  covalent geometry    : angle       0.61351 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 THR cc_start: 0.7504 (p) cc_final: 0.7298 (t)
REVERT: A  158 MET cc_start: 0.6851 (tmm) cc_final: 0.6639 (tmm)
REVERT: A  193 ASN cc_start: 0.8923 (m-40) cc_final: 0.8471 (m-40)
REVERT: B  250 HIS cc_start: 0.6203 (t70) cc_final: 0.5854 (t70)
REVERT: B  293 TYR cc_start: 0.5379 (t80) cc_final: 0.5124 (t80)
REVERT: B  322 TYR cc_start: 0.7291 (t80) cc_final: 0.5995 (t80)
REVERT: B  335 ASP cc_start: 0.8349 (t0) cc_final: 0.8113 (t0)
REVERT: B  385 ASP cc_start: 0.6834 (t70) cc_final: 0.6387 (m-30)
REVERT: B  389 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7216 (mptt)
REVERT: B  487 MET cc_start: 0.5444 (tmm) cc_final: 0.5110 (tmm)
REVERT: C  142 LEU cc_start: 0.8785 (mt) cc_final: 0.8570 (mt)
REVERT: C  147 ILE cc_start: 0.8272 (mm) cc_final: 0.7944 (mm)
REVERT: C  176 LEU cc_start: 0.7703 (mt) cc_final: 0.7176 (tt)
REVERT: C  193 ASN cc_start: 0.8967 (m-40) cc_final: 0.8322 (m-40)
REVERT: D  275 GLU cc_start: 0.7125 (pt0) cc_final: 0.6793 (pm20)
REVERT: D  314 LEU cc_start: 0.9270 (mt) cc_final: 0.9063 (mt)
REVERT: D  322 TYR cc_start: 0.7231 (t80) cc_final: 0.5405 (t80)
REVERT: D  335 ASP cc_start: 0.8454 (t0) cc_final: 0.8051 (t0)
REVERT: D  389 LYS cc_start: 0.8465 (mmtt) cc_final: 0.7370 (mptt)
REVERT: D  436 TYR cc_start: 0.7354 (t80) cc_final: 0.7044 (t80)
REVERT: D  551 ASP cc_start: 0.6958 (m-30) cc_final: 0.6362 (t70)
REVERT: E  142 LEU cc_start: 0.8800 (mt) cc_final: 0.8551 (mt)
REVERT: E  147 ILE cc_start: 0.8525 (mm) cc_final: 0.8231 (mm)
REVERT: E  176 LEU cc_start: 0.7677 (mt) cc_final: 0.7448 (tt)
REVERT: F  302 MET cc_start: 0.7321 (mmm) cc_final: 0.6964 (mmt)
REVERT: F  312 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7697 (tp-100)
REVERT: F  389 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7437 (mptt)
REVERT: F  430 TYR cc_start: 0.8410 (m-80) cc_final: 0.7883 (m-80)
REVERT: F  446 CYS cc_start: 0.4164 (t) cc_final: 0.3948 (t)
REVERT: F  463 MET cc_start: 0.6281 (ttm) cc_final: 0.5437 (ttm)
REVERT: F  487 MET cc_start: 0.5661 (tmm) cc_final: 0.5394 (tmm)
REVERT: F  551 ASP cc_start: 0.6801 (m-30) cc_final: 0.5850 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.2040
  time to fit residues: 85.4077
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 114 optimal weight:   10.0000
   chunk 49 optimal weight:    0.3980
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
C 138 HIS
D 312 GLN
D 468 GLN
** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS
F 296 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.159627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.136874 restraints weight = 19922.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.140180 restraints weight = 13275.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.142615 restraints weight = 9790.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9993  Z= 0.182
  Angle     :  0.681   6.754  13578  Z= 0.361
  Chirality :  0.048   0.209   1647
  Planarity :  0.004   0.042   1716
  Dihedral  :  6.072  32.523   1377
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.80 (0.23), residues: 1281
  helix:  0.26 (0.29), residues: 327
  sheet: -2.30 (0.42), residues: 117
  loop : -1.72 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP D 423 
 HIS   0.004   0.001   HIS F 250 
 PHE   0.024   0.002   PHE F 491 
 TYR   0.022   0.002   TYR F 293 
 ARG   0.005   0.001   ARG B 547 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04964 (  330)
  hydrogen bonds       : angle       5.63528 (  891)
  SS BOND              : bond        0.00417 (   15)
  SS BOND              : angle       1.81961 (   30)
  covalent geometry    : bond        0.00408 ( 9978)
  covalent geometry    : angle       0.67629 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8957 (mt) cc_final: 0.8738 (mt)
REVERT: A  158 MET cc_start: 0.6737 (tmm) cc_final: 0.6297 (tmm)
REVERT: A  176 LEU cc_start: 0.7654 (mt) cc_final: 0.7337 (tt)
REVERT: A  193 ASN cc_start: 0.9064 (m-40) cc_final: 0.8719 (m-40)
REVERT: B  250 HIS cc_start: 0.6262 (t70) cc_final: 0.5912 (t70)
REVERT: B  314 LEU cc_start: 0.9252 (mt) cc_final: 0.9037 (mt)
REVERT: B  322 TYR cc_start: 0.7459 (t80) cc_final: 0.5876 (t80)
REVERT: B  335 ASP cc_start: 0.8344 (t0) cc_final: 0.8074 (t0)
REVERT: B  385 ASP cc_start: 0.6927 (t70) cc_final: 0.6592 (m-30)
REVERT: B  389 LYS cc_start: 0.8535 (mmtt) cc_final: 0.7558 (mptt)
REVERT: B  487 MET cc_start: 0.5426 (tmm) cc_final: 0.5158 (tmm)
REVERT: C  142 LEU cc_start: 0.8915 (mt) cc_final: 0.8691 (mt)
REVERT: C  147 ILE cc_start: 0.8352 (mm) cc_final: 0.8012 (mm)
REVERT: C  193 ASN cc_start: 0.9011 (m-40) cc_final: 0.8382 (m-40)
REVERT: D  275 GLU cc_start: 0.7117 (pt0) cc_final: 0.6827 (pm20)
REVERT: D  322 TYR cc_start: 0.7475 (t80) cc_final: 0.5554 (t80)
REVERT: D  335 ASP cc_start: 0.8246 (t0) cc_final: 0.7874 (t0)
REVERT: D  436 TYR cc_start: 0.7415 (t80) cc_final: 0.7069 (t80)
REVERT: D  463 MET cc_start: 0.6850 (ttm) cc_final: 0.6398 (ttm)
REVERT: D  487 MET cc_start: 0.5942 (tmm) cc_final: 0.5706 (tmm)
REVERT: D  537 ILE cc_start: 0.8741 (tt) cc_final: 0.8445 (tt)
REVERT: D  551 ASP cc_start: 0.7225 (m-30) cc_final: 0.6680 (t70)
REVERT: E  142 LEU cc_start: 0.8905 (mt) cc_final: 0.8648 (mt)
REVERT: E  147 ILE cc_start: 0.8630 (mm) cc_final: 0.8282 (mm)
REVERT: F  305 MET cc_start: 0.2922 (mpp) cc_final: 0.2661 (mtm)
REVERT: F  312 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7919 (tp-100)
REVERT: F  389 LYS cc_start: 0.8594 (mmtt) cc_final: 0.7766 (mptt)
REVERT: F  463 MET cc_start: 0.6594 (ttm) cc_final: 0.6290 (ttm)
REVERT: F  487 MET cc_start: 0.5786 (tmm) cc_final: 0.5475 (tmm)
REVERT: F  551 ASP cc_start: 0.7039 (m-30) cc_final: 0.6300 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.1939
  time to fit residues: 78.5945
Evaluate side-chains
  219 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 73 optimal weight:    0.0020
   chunk 83 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0370
   chunk 51 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.8072

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

Flipped N/Q/H residues before XYZ refinement:
C 138 HIS
C 209 ASN
D 468 GLN
E 138 HIS
** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 296 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.162798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.140690 restraints weight = 19828.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.144120 restraints weight = 12995.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.146615 restraints weight = 9414.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9993  Z= 0.128
  Angle     :  0.624   8.738  13578  Z= 0.330
  Chirality :  0.046   0.240   1647
  Planarity :  0.004   0.045   1716
  Dihedral  :  5.730  27.409   1377
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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: -1.63 (0.23), residues: 1281
  helix:  0.66 (0.29), residues: 321
  sheet: -2.03 (0.44), residues: 117
  loop : -1.73 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 423 
 HIS   0.002   0.001   HIS F 250 
 PHE   0.008   0.002   PHE F 448 
 TYR   0.013   0.001   TYR F 293 
 ARG   0.008   0.001   ARG B 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  330)
  hydrogen bonds       : angle       5.39189 (  891)
  SS BOND              : bond        0.00606 (   15)
  SS BOND              : angle       1.79459 (   30)
  covalent geometry    : bond        0.00281 ( 9978)
  covalent geometry    : angle       0.61942 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LEU cc_start: 0.7401 (mt) cc_final: 0.7165 (tt)
REVERT: A  193 ASN cc_start: 0.9009 (m-40) cc_final: 0.8572 (m-40)
REVERT: B  250 HIS cc_start: 0.6285 (t70) cc_final: 0.6031 (t70)
REVERT: B  314 LEU cc_start: 0.9164 (mt) cc_final: 0.8930 (mt)
REVERT: B  322 TYR cc_start: 0.7320 (t80) cc_final: 0.6144 (t80)
REVERT: B  335 ASP cc_start: 0.8350 (t0) cc_final: 0.8040 (t0)
REVERT: B  389 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7451 (mptt)
REVERT: B  463 MET cc_start: 0.6996 (ttm) cc_final: 0.6773 (ttm)
REVERT: B  487 MET cc_start: 0.5452 (tmm) cc_final: 0.5141 (tmm)
REVERT: C  193 ASN cc_start: 0.9050 (m-40) cc_final: 0.8454 (m-40)
REVERT: D  275 GLU cc_start: 0.7128 (pt0) cc_final: 0.6904 (pm20)
REVERT: D  322 TYR cc_start: 0.7434 (t80) cc_final: 0.5726 (t80)
REVERT: D  335 ASP cc_start: 0.8322 (t0) cc_final: 0.7858 (t0)
REVERT: D  436 TYR cc_start: 0.7374 (t80) cc_final: 0.7063 (t80)
REVERT: D  463 MET cc_start: 0.6910 (ttm) cc_final: 0.6581 (ttm)
REVERT: D  487 MET cc_start: 0.6045 (tmm) cc_final: 0.5753 (tmm)
REVERT: D  508 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8044 (ttpt)
REVERT: D  551 ASP cc_start: 0.7008 (m-30) cc_final: 0.6259 (t70)
REVERT: E  142 LEU cc_start: 0.8863 (mt) cc_final: 0.8653 (mt)
REVERT: E  147 ILE cc_start: 0.8619 (mm) cc_final: 0.8257 (mm)
REVERT: F  305 MET cc_start: 0.2904 (mpp) cc_final: 0.2549 (mtm)
REVERT: F  389 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7646 (mptt)
REVERT: F  463 MET cc_start: 0.6663 (ttm) cc_final: 0.6432 (ttm)
REVERT: F  487 MET cc_start: 0.5719 (tmm) cc_final: 0.5394 (tmm)
REVERT: F  551 ASP cc_start: 0.7076 (m-30) cc_final: 0.5984 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1848
  time to fit residues: 75.2132
Evaluate side-chains
  225 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0770
   chunk 15 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0980
   chunk 69 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 114 optimal weight:   10.0000
   chunk 49 optimal weight:    0.3980
   overall best weight:    2.5142

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
D 468 GLN
E 138 HIS
F 296 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.160892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.138395 restraints weight = 19843.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.141682 restraints weight = 13181.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.144106 restraints weight = 9710.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.4660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9993  Z= 0.150
  Angle     :  0.658   6.877  13578  Z= 0.348
  Chirality :  0.047   0.261   1647
  Planarity :  0.004   0.043   1716
  Dihedral  :  5.763  26.329   1377
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.23), residues: 1281
  helix:  0.57 (0.29), residues: 333
  sheet: -1.96 (0.44), residues: 117
  loop : -1.62 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 423 
 HIS   0.002   0.001   HIS E 138 
 PHE   0.008   0.002   PHE D 329 
 TYR   0.017   0.002   TYR F 293 
 ARG   0.008   0.001   ARG B 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04498 (  330)
  hydrogen bonds       : angle       5.51267 (  891)
  SS BOND              : bond        0.00586 (   15)
  SS BOND              : angle       1.78242 (   30)
  covalent geometry    : bond        0.00329 ( 9978)
  covalent geometry    : angle       0.65292 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  250 HIS cc_start: 0.6094 (t70) cc_final: 0.5863 (t70)
REVERT: B  322 TYR cc_start: 0.7402 (t80) cc_final: 0.6046 (t80)
REVERT: B  335 ASP cc_start: 0.8365 (t0) cc_final: 0.7966 (t0)
REVERT: B  385 ASP cc_start: 0.7499 (m-30) cc_final: 0.7294 (m-30)
REVERT: B  389 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7649 (mptt)
REVERT: B  487 MET cc_start: 0.5607 (tmm) cc_final: 0.5334 (tmm)
REVERT: B  508 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7951 (ttpt)
REVERT: C  193 ASN cc_start: 0.9049 (m-40) cc_final: 0.8395 (m-40)
REVERT: D  275 GLU cc_start: 0.7119 (pt0) cc_final: 0.6836 (pm20)
REVERT: D  322 TYR cc_start: 0.7364 (t80) cc_final: 0.5675 (t80)
REVERT: D  335 ASP cc_start: 0.8308 (t0) cc_final: 0.7777 (t0)
REVERT: D  436 TYR cc_start: 0.7389 (t80) cc_final: 0.7050 (t80)
REVERT: D  463 MET cc_start: 0.7074 (ttm) cc_final: 0.6863 (ttm)
REVERT: D  487 MET cc_start: 0.5829 (tmm) cc_final: 0.5538 (tmm)
REVERT: D  508 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8094 (ttpt)
REVERT: D  551 ASP cc_start: 0.7072 (m-30) cc_final: 0.6181 (t70)
REVERT: E  142 LEU cc_start: 0.8877 (mt) cc_final: 0.8674 (mt)
REVERT: E  147 ILE cc_start: 0.8614 (mm) cc_final: 0.8234 (mm)
REVERT: E  193 ASN cc_start: 0.8771 (m-40) cc_final: 0.8558 (m-40)
REVERT: F  305 MET cc_start: 0.2921 (mpp) cc_final: 0.2580 (mtm)
REVERT: F  389 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7725 (mptt)
REVERT: F  487 MET cc_start: 0.5887 (tmm) cc_final: 0.5499 (tmm)
REVERT: F  551 ASP cc_start: 0.7130 (m-30) cc_final: 0.5956 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.1978
  time to fit residues: 77.2334
Evaluate side-chains
  229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 123 optimal weight:    9.9990
   chunk 114 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 574 ASN
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
E 138 HIS
** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.163029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140013 restraints weight = 20134.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.143669 restraints weight = 12852.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.146302 restraints weight = 9122.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9993  Z= 0.131
  Angle     :  0.642   7.728  13578  Z= 0.338
  Chirality :  0.047   0.303   1647
  Planarity :  0.004   0.041   1716
  Dihedral  :  5.663  24.387   1377
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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: -1.41 (0.23), residues: 1281
  helix:  0.75 (0.29), residues: 321
  sheet: -1.83 (0.44), residues: 117
  loop : -1.57 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 423 
 HIS   0.003   0.001   HIS C 138 
 PHE   0.008   0.002   PHE F 526 
 TYR   0.025   0.001   TYR F 322 
 ARG   0.006   0.001   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04360 (  330)
  hydrogen bonds       : angle       5.40091 (  891)
  SS BOND              : bond        0.00426 (   15)
  SS BOND              : angle       1.60061 (   30)
  covalent geometry    : bond        0.00280 ( 9978)
  covalent geometry    : angle       0.63785 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  308 GLU cc_start: 0.5246 (mp0) cc_final: 0.4981 (mp0)
REVERT: B  322 TYR cc_start: 0.7390 (t80) cc_final: 0.6040 (t80)
REVERT: B  335 ASP cc_start: 0.8338 (t0) cc_final: 0.8050 (t0)
REVERT: B  340 GLU cc_start: 0.7175 (pm20) cc_final: 0.6971 (pm20)
REVERT: B  389 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7733 (mptt)
REVERT: B  487 MET cc_start: 0.5439 (tmm) cc_final: 0.5180 (tmm)
REVERT: B  508 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7974 (ttpt)
REVERT: B  567 GLU cc_start: 0.6502 (mm-30) cc_final: 0.6197 (mm-30)
REVERT: C  193 ASN cc_start: 0.9059 (m-40) cc_final: 0.8492 (m-40)
REVERT: D  275 GLU cc_start: 0.7131 (pt0) cc_final: 0.6865 (pm20)
REVERT: D  314 LEU cc_start: 0.9287 (mt) cc_final: 0.9085 (mt)
REVERT: D  322 TYR cc_start: 0.7516 (t80) cc_final: 0.5767 (t80)
REVERT: D  335 ASP cc_start: 0.8208 (t0) cc_final: 0.7576 (t0)
REVERT: D  436 TYR cc_start: 0.7590 (t80) cc_final: 0.7270 (t80)
REVERT: D  487 MET cc_start: 0.5830 (tmm) cc_final: 0.5524 (tmm)
REVERT: D  508 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7987 (ttpt)
REVERT: D  510 TYR cc_start: 0.7155 (t80) cc_final: 0.6650 (t80)
REVERT: D  551 ASP cc_start: 0.7059 (m-30) cc_final: 0.6335 (t70)
REVERT: E  147 ILE cc_start: 0.8640 (mm) cc_final: 0.8295 (mm)
REVERT: E  193 ASN cc_start: 0.8772 (m-40) cc_final: 0.8519 (m-40)
REVERT: F  305 MET cc_start: 0.2920 (mpp) cc_final: 0.2508 (mtm)
REVERT: F  389 LYS cc_start: 0.8585 (mmtt) cc_final: 0.7763 (mptt)
REVERT: F  487 MET cc_start: 0.5849 (tmm) cc_final: 0.5431 (tmm)
REVERT: F  547 ARG cc_start: 0.5152 (tpp-160) cc_final: 0.4910 (mmt-90)
REVERT: F  551 ASP cc_start: 0.7097 (m-30) cc_final: 0.6000 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.2080
  time to fit residues: 83.4341
Evaluate side-chains
  234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 120 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 ASN
A 209 ASN
B 344 GLN
B 468 GLN
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
E 138 HIS
** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.162327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139602 restraints weight = 20188.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.143230 restraints weight = 12825.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.145786 restraints weight = 9123.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.5027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9993  Z= 0.142
  Angle     :  0.663   8.637  13578  Z= 0.348
  Chirality :  0.048   0.337   1647
  Planarity :  0.004   0.039   1716
  Dihedral  :  5.639  24.050   1377
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.17 %
    Favored  : 98.65 %
  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: -1.54 (0.23), residues: 1281
  helix:  0.52 (0.28), residues: 336
  sheet: -1.66 (0.45), residues: 117
  loop : -1.68 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 423 
 HIS   0.002   0.001   HIS D 409 
 PHE   0.010   0.002   PHE F 526 
 TYR   0.013   0.001   TYR F 293 
 ARG   0.006   0.001   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  330)
  hydrogen bonds       : angle       5.48169 (  891)
  SS BOND              : bond        0.00415 (   15)
  SS BOND              : angle       1.77245 (   30)
  covalent geometry    : bond        0.00308 ( 9978)
  covalent geometry    : angle       0.65885 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 281
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  308 GLU cc_start: 0.5225 (mp0) cc_final: 0.4980 (mp0)
REVERT: B  314 LEU cc_start: 0.9278 (mt) cc_final: 0.9063 (mt)
REVERT: B  322 TYR cc_start: 0.7382 (t80) cc_final: 0.6022 (t80)
REVERT: B  335 ASP cc_start: 0.8332 (t0) cc_final: 0.8050 (t0)
REVERT: B  493 LEU cc_start: 0.6290 (tp) cc_final: 0.6088 (tp)
REVERT: B  508 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7945 (ttpt)
REVERT: B  567 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6238 (mm-30)
REVERT: C  193 ASN cc_start: 0.9010 (m-40) cc_final: 0.8388 (m-40)
REVERT: D  250 HIS cc_start: 0.6750 (t70) cc_final: 0.6543 (t70)
REVERT: D  322 TYR cc_start: 0.7401 (t80) cc_final: 0.5692 (t80)
REVERT: D  335 ASP cc_start: 0.8261 (t0) cc_final: 0.7623 (t0)
REVERT: D  340 GLU cc_start: 0.7168 (pm20) cc_final: 0.6957 (pm20)
REVERT: D  436 TYR cc_start: 0.7537 (t80) cc_final: 0.7236 (t80)
REVERT: D  463 MET cc_start: 0.6586 (ttm) cc_final: 0.6057 (ttm)
REVERT: D  487 MET cc_start: 0.5894 (tmm) cc_final: 0.5588 (tmm)
REVERT: D  510 TYR cc_start: 0.7156 (t80) cc_final: 0.6706 (t80)
REVERT: D  551 ASP cc_start: 0.7197 (m-30) cc_final: 0.6275 (t70)
REVERT: E  142 LEU cc_start: 0.8915 (mt) cc_final: 0.8695 (mt)
REVERT: E  193 ASN cc_start: 0.8752 (m-40) cc_final: 0.8502 (m-40)
REVERT: F  308 GLU cc_start: 0.5753 (mp0) cc_final: 0.5397 (mp0)
REVERT: F  389 LYS cc_start: 0.8754 (mmtt) cc_final: 0.7832 (mptt)
REVERT: F  487 MET cc_start: 0.5936 (tmm) cc_final: 0.5480 (tmm)
REVERT: F  527 ILE cc_start: 0.8677 (mp) cc_final: 0.8240 (mp)
REVERT: F  551 ASP cc_start: 0.7126 (m-30) cc_final: 0.6231 (t70)
  outliers start: 2
  outliers final: 0
  residues processed: 283
  average time/residue: 0.1933
  time to fit residues: 78.1260
Evaluate side-chains
  233 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0970
   chunk 54 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0670
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.4314

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
D 574 ASN
E 138 HIS
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 574 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.166773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.144108 restraints weight = 19753.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.147857 restraints weight = 12524.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.150439 restraints weight = 8888.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9993  Z= 0.121
  Angle     :  0.655   7.994  13578  Z= 0.344
  Chirality :  0.048   0.310   1647
  Planarity :  0.004   0.041   1716
  Dihedral  :  5.377  22.131   1377
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.08 %
  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: -1.39 (0.23), residues: 1281
  helix:  0.56 (0.28), residues: 336
  sheet: -1.48 (0.46), residues: 117
  loop : -1.54 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 423 
 HIS   0.003   0.000   HIS A 138 
 PHE   0.008   0.002   PHE D 526 
 TYR   0.011   0.001   TYR B 321 
 ARG   0.007   0.001   ARG D 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04232 (  330)
  hydrogen bonds       : angle       5.26863 (  891)
  SS BOND              : bond        0.00355 (   15)
  SS BOND              : angle       1.56560 (   30)
  covalent geometry    : bond        0.00253 ( 9978)
  covalent geometry    : angle       0.65179 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8615 (mm) cc_final: 0.8380 (mm)
REVERT: A  195 VAL cc_start: 0.8759 (t) cc_final: 0.8401 (t)
REVERT: B  322 TYR cc_start: 0.7113 (t80) cc_final: 0.5924 (t80)
REVERT: B  335 ASP cc_start: 0.8347 (t0) cc_final: 0.8021 (t0)
REVERT: B  340 GLU cc_start: 0.7256 (pm20) cc_final: 0.7031 (pm20)
REVERT: B  389 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7201 (mppt)
REVERT: B  487 MET cc_start: 0.5932 (tmm) cc_final: 0.5708 (tmm)
REVERT: B  567 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5950 (mm-30)
REVERT: C  193 ASN cc_start: 0.9007 (m-40) cc_final: 0.8446 (m-40)
REVERT: D  250 HIS cc_start: 0.6582 (t70) cc_final: 0.6379 (t70)
REVERT: D  322 TYR cc_start: 0.7329 (t80) cc_final: 0.5635 (t80)
REVERT: D  335 ASP cc_start: 0.8228 (t0) cc_final: 0.7660 (t0)
REVERT: D  340 GLU cc_start: 0.7092 (pm20) cc_final: 0.6892 (pm20)
REVERT: D  371 ILE cc_start: 0.8453 (mm) cc_final: 0.8094 (mp)
REVERT: D  394 SER cc_start: 0.7757 (t) cc_final: 0.7161 (p)
REVERT: D  436 TYR cc_start: 0.7417 (t80) cc_final: 0.7187 (t80)
REVERT: D  487 MET cc_start: 0.5791 (tmm) cc_final: 0.5548 (tmm)
REVERT: D  510 TYR cc_start: 0.7362 (t80) cc_final: 0.6969 (t80)
REVERT: D  532 CYS cc_start: 0.4956 (p) cc_final: 0.4500 (t)
REVERT: D  551 ASP cc_start: 0.6905 (m-30) cc_final: 0.6307 (t70)
REVERT: E  142 LEU cc_start: 0.8795 (mt) cc_final: 0.8580 (mt)
REVERT: F  308 GLU cc_start: 0.5603 (mp0) cc_final: 0.5341 (mp0)
REVERT: F  314 LEU cc_start: 0.9081 (mt) cc_final: 0.8879 (mt)
REVERT: F  389 LYS cc_start: 0.8698 (mmtt) cc_final: 0.7759 (mptt)
REVERT: F  487 MET cc_start: 0.5812 (tmm) cc_final: 0.5451 (tmm)
REVERT: F  551 ASP cc_start: 0.7187 (m-30) cc_final: 0.6186 (t70)
REVERT: F  570 ASP cc_start: 0.7837 (m-30) cc_final: 0.7457 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1920
  time to fit residues: 78.3133
Evaluate side-chains
  237 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    0.0020
   chunk 4 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 81 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 21 optimal weight:    0.1980
   chunk 106 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    1.3792

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

Flipped N/Q/H residues before XYZ refinement:
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
D 409 HIS
** F 468 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 = 0.4201 r_free = 0.4201 target = 0.164885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.141703 restraints weight = 19756.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.145343 restraints weight = 12635.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.147923 restraints weight = 9045.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.5394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9993  Z= 0.129
  Angle     :  0.674   8.683  13578  Z= 0.353
  Chirality :  0.048   0.304   1647
  Planarity :  0.004   0.038   1716
  Dihedral  :  5.387  23.399   1377
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -1.31 (0.23), residues: 1281
  helix:  0.62 (0.29), residues: 330
  sheet: -1.41 (0.46), residues: 117
  loop : -1.49 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 423 
 HIS   0.002   0.001   HIS A 138 
 PHE   0.011   0.002   PHE F 491 
 TYR   0.011   0.001   TYR B 424 
 ARG   0.006   0.001   ARG F 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04416 (  330)
  hydrogen bonds       : angle       5.32095 (  891)
  SS BOND              : bond        0.00418 (   15)
  SS BOND              : angle       2.17681 (   30)
  covalent geometry    : bond        0.00277 ( 9978)
  covalent geometry    : angle       0.66647 (13548)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8638 (mm) cc_final: 0.8387 (mm)
REVERT: A  195 VAL cc_start: 0.8789 (t) cc_final: 0.8359 (t)
REVERT: B  314 LEU cc_start: 0.9271 (mt) cc_final: 0.9052 (mt)
REVERT: B  322 TYR cc_start: 0.7314 (t80) cc_final: 0.5960 (t80)
REVERT: B  335 ASP cc_start: 0.8285 (t0) cc_final: 0.7989 (t0)
REVERT: B  340 GLU cc_start: 0.7355 (pm20) cc_final: 0.7069 (pm20)
REVERT: B  389 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8133 (mmtp)
REVERT: B  408 VAL cc_start: 0.8318 (t) cc_final: 0.8102 (t)
REVERT: B  487 MET cc_start: 0.5505 (tmm) cc_final: 0.5287 (tmm)
REVERT: B  510 TYR cc_start: 0.6822 (t80) cc_final: 0.6476 (t80)
REVERT: B  567 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5996 (mm-30)
REVERT: C  158 MET cc_start: 0.6407 (tpp) cc_final: 0.5767 (tpt)
REVERT: C  193 ASN cc_start: 0.8978 (m-40) cc_final: 0.8436 (m-40)
REVERT: D  250 HIS cc_start: 0.6496 (t70) cc_final: 0.6294 (t70)
REVERT: D  314 LEU cc_start: 0.9290 (mt) cc_final: 0.9084 (mt)
REVERT: D  335 ASP cc_start: 0.8243 (t0) cc_final: 0.7646 (t0)
REVERT: D  340 GLU cc_start: 0.7193 (pm20) cc_final: 0.6961 (pm20)
REVERT: D  371 ILE cc_start: 0.8485 (mm) cc_final: 0.8074 (mp)
REVERT: D  389 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8286 (mmtt)
REVERT: D  394 SER cc_start: 0.7807 (t) cc_final: 0.7161 (p)
REVERT: D  436 TYR cc_start: 0.7439 (t80) cc_final: 0.7218 (t80)
REVERT: D  487 MET cc_start: 0.5864 (tmm) cc_final: 0.5616 (tmm)
REVERT: D  510 TYR cc_start: 0.7465 (t80) cc_final: 0.7092 (t80)
REVERT: D  532 CYS cc_start: 0.4998 (p) cc_final: 0.4482 (t)
REVERT: D  551 ASP cc_start: 0.6888 (m-30) cc_final: 0.6190 (t70)
REVERT: E  193 ASN cc_start: 0.8429 (m-40) cc_final: 0.8222 (m-40)
REVERT: F  314 LEU cc_start: 0.9084 (mt) cc_final: 0.8875 (mt)
REVERT: F  321 TYR cc_start: 0.7910 (t80) cc_final: 0.7609 (t80)
REVERT: F  371 ILE cc_start: 0.8533 (mm) cc_final: 0.8331 (mp)
REVERT: F  411 LEU cc_start: 0.8497 (mt) cc_final: 0.7707 (tt)
REVERT: F  487 MET cc_start: 0.5869 (tmm) cc_final: 0.5482 (tmm)
REVERT: F  508 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7787 (ttpt)
REVERT: F  551 ASP cc_start: 0.7294 (m-30) cc_final: 0.6277 (t70)
REVERT: F  570 ASP cc_start: 0.7807 (m-30) cc_final: 0.7437 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1908
  time to fit residues: 76.7415
Evaluate side-chains
  235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    0.2980
   chunk 9 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 344 GLN
E 138 HIS
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 468 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 = 0.4210 r_free = 0.4210 target = 0.166465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.144197 restraints weight = 20129.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.147527 restraints weight = 13204.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.150025 restraints weight = 9626.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.5567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9993  Z= 0.120
  Angle     :  0.656   7.925  13578  Z= 0.344
  Chirality :  0.048   0.296   1647
  Planarity :  0.004   0.040   1716
  Dihedral  :  5.301  21.740   1377
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.23), residues: 1281
  helix:  0.81 (0.30), residues: 318
  sheet: -1.31 (0.46), residues: 117
  loop : -1.43 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 423 
 HIS   0.002   0.000   HIS A 138 
 PHE   0.011   0.002   PHE F 329 
 TYR   0.020   0.001   TYR D 322 
 ARG   0.007   0.001   ARG F 277 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  330)
  hydrogen bonds       : angle       5.28507 (  891)
  SS BOND              : bond        0.00397 (   15)
  SS BOND              : angle       1.96726 (   30)
  covalent geometry    : bond        0.00256 ( 9978)
  covalent geometry    : angle       0.64985 (13548)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3189.34 seconds
wall clock time: 56 minutes 9.08 seconds (3369.08 seconds total)