Starting phenix.real_space_refine
on Wed Mar  4 00:43:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xye_10649/03_2026/6xye_10649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xye_10649/03_2026/6xye_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_10649/03_2026/6xye_10649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2026/6xye_10649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2026/6xye_10649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2026/6xye_10649.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    C, E, D, F
  Time building chain proxies: 1.76, per 1000 atoms: 0.18
  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: 0.69
  Conformation dependent library (CDL) restraints added in 399.9 milliseconds
  

  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: 0.39
  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: 1.29

  Time building geometry restraints manager: 0.96 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

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:             0.260
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.140
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG F 480 
 TYR   0.027   0.004   TYR B 293 
 PHE   0.016   0.003   PHE F 448 
 TRP   0.025   0.006   TRP E 139 
 HIS   0.012   0.002   HIS F 409 

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

*********************** 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  : 0.230 
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: 0.7387 (t0) cc_final: 0.7111 (t0)
REVERT: A  193 ASN cc_start: 0.8737 (m-40) cc_final: 0.8247 (m-40)
REVERT: B  322 TYR cc_start: 0.7310 (t80) cc_final: 0.5898 (t80)
REVERT: B  385 ASP cc_start: 0.6926 (t70) cc_final: 0.6682 (m-30)
REVERT: B  389 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7391 (mptt)
REVERT: B  411 LEU cc_start: 0.8406 (mt) cc_final: 0.8123 (mp)
REVERT: B  412 GLU cc_start: 0.8062 (tp30) cc_final: 0.7506 (tp30)
REVERT: B  460 LEU cc_start: 0.9091 (mt) cc_final: 0.8782 (tt)
REVERT: B  463 MET cc_start: 0.6901 (ttm) cc_final: 0.5341 (ttm)
REVERT: C  142 LEU cc_start: 0.9009 (mt) cc_final: 0.8707 (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: 0.8160 (m-40)
REVERT: D  389 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7524 (mptt)
REVERT: D  436 TYR cc_start: 0.6971 (t80) cc_final: 0.6659 (t80)
REVERT: D  463 MET cc_start: 0.6951 (ttm) cc_final: 0.5708 (ttm)
REVERT: D  551 ASP cc_start: 0.7377 (m-30) cc_final: 0.6746 (t70)
REVERT: D  580 LYS cc_start: 0.9177 (tttt) cc_final: 0.8485 (mttm)
REVERT: E  142 LEU cc_start: 0.9012 (mt) cc_final: 0.8706 (mt)
REVERT: E  173 ASN cc_start: 0.7548 (t0) cc_final: 0.7312 (t0)
REVERT: E  193 ASN cc_start: 0.8685 (m-40) cc_final: 0.8468 (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: 0.6953 (mmt)
REVERT: F  389 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7584 (mptt)
REVERT: F  422 GLU cc_start: 0.6669 (tt0) cc_final: 0.6319 (mp0)
REVERT: F  430 TYR cc_start: 0.8340 (m-80) cc_final: 0.8057 (m-80)
REVERT: F  436 TYR cc_start: 0.7039 (t80) cc_final: 0.6800 (t80)
REVERT: F  463 MET cc_start: 0.6671 (ttm) cc_final: 0.5418 (ttm)
REVERT: F  510 TYR cc_start: 0.7010 (t80) cc_final: 0.6362 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 380
  average time/residue: 0.1018
  time to fit residues: 53.1015
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  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.7982

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.163988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.141112 restraints weight = 19470.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.144669 restraints weight = 12814.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.147247 restraints weight = 9370.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.149117 restraints weight = 7316.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.150352 restraints weight = 6037.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9993  Z= 0.156
  Angle     :  0.694   7.782  13578  Z= 0.367
  Chirality :  0.048   0.326   1647
  Planarity :  0.004   0.032   1716
  Dihedral  :  6.531  36.318   1377
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.22), residues: 1281
  helix: -0.54 (0.26), residues: 360
  sheet: -2.61 (0.49), residues: 87
  loop : -1.74 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 277 
 TYR   0.017   0.002   TYR D 424 
 PHE   0.010   0.002   PHE D 329 
 TRP   0.013   0.002   TRP B 423 
 HIS   0.003   0.001   HIS D 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9978)
  covalent geometry    : angle       0.68618 (13548)
  SS BOND              : bond        0.01172 (   15)
  SS BOND              : angle       2.36616 (   30)
  hydrogen bonds       : bond        0.05269 (  330)
  hydrogen bonds       : angle       5.74493 (  891)

*********************** 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
  301 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8888 (mt) cc_final: 0.8590 (mt)
REVERT: A  147 ILE cc_start: 0.8504 (mm) cc_final: 0.8281 (mm)
REVERT: A  193 ASN cc_start: 0.8936 (m-40) cc_final: 0.8432 (m-40)
REVERT: B  322 TYR cc_start: 0.7433 (t80) cc_final: 0.5995 (t80)
REVERT: B  385 ASP cc_start: 0.6640 (t70) cc_final: 0.6334 (m-30)
REVERT: B  389 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7274 (mptt)
REVERT: B  412 GLU cc_start: 0.8299 (tp30) cc_final: 0.7589 (tp30)
REVERT: B  463 MET cc_start: 0.6692 (ttm) cc_final: 0.6381 (ttm)
REVERT: B  487 MET cc_start: 0.5672 (tmm) cc_final: 0.5453 (tmm)
REVERT: B  551 ASP cc_start: 0.7295 (m-30) cc_final: 0.6785 (t70)
REVERT: C  142 LEU cc_start: 0.8818 (mt) cc_final: 0.8595 (mt)
REVERT: C  147 ILE cc_start: 0.8316 (mm) cc_final: 0.8011 (mm)
REVERT: C  176 LEU cc_start: 0.7791 (mt) cc_final: 0.7257 (tt)
REVERT: C  193 ASN cc_start: 0.8966 (m-40) cc_final: 0.8359 (m-40)
REVERT: D  275 GLU cc_start: 0.7173 (pt0) cc_final: 0.6777 (pm20)
REVERT: D  389 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7446 (mptt)
REVERT: D  436 TYR cc_start: 0.7332 (t80) cc_final: 0.6932 (t80)
REVERT: D  551 ASP cc_start: 0.7027 (m-30) cc_final: 0.6191 (t70)
REVERT: E  142 LEU cc_start: 0.8740 (mt) cc_final: 0.8527 (mt)
REVERT: E  147 ILE cc_start: 0.8524 (mm) cc_final: 0.8266 (mm)
REVERT: F  302 MET cc_start: 0.7404 (mmm) cc_final: 0.7129 (mmt)
REVERT: F  312 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7731 (tp-100)
REVERT: F  314 LEU cc_start: 0.9255 (mt) cc_final: 0.9052 (mt)
REVERT: F  385 ASP cc_start: 0.8099 (m-30) cc_final: 0.7749 (m-30)
REVERT: F  389 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7597 (mptt)
REVERT: F  430 TYR cc_start: 0.8342 (m-80) cc_final: 0.7740 (m-80)
REVERT: F  436 TYR cc_start: 0.7320 (t80) cc_final: 0.7115 (t80)
REVERT: F  508 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7701 (mtmm)
REVERT: F  510 TYR cc_start: 0.6851 (t80) cc_final: 0.6386 (t80)
REVERT: F  551 ASP cc_start: 0.7466 (m-30) cc_final: 0.6608 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 301
  average time/residue: 0.0901
  time to fit residues: 38.3496
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  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 56 optimal weight:    0.0030
   chunk 21 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.1192

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

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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.165607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.143628 restraints weight = 19404.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.147037 restraints weight = 12896.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.149520 restraints weight = 9406.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.151261 restraints weight = 7356.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.152600 restraints weight = 6063.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6831
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9993  Z= 0.119
  Angle     :  0.617   6.584  13578  Z= 0.327
  Chirality :  0.046   0.202   1647
  Planarity :  0.004   0.039   1716
  Dihedral  :  5.895  27.109   1377
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.23), residues: 1281
  helix:  0.03 (0.28), residues: 333
  sheet: -1.98 (0.43), residues: 117
  loop : -1.80 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 547 
 TYR   0.013   0.001   TYR D 424 
 PHE   0.018   0.002   PHE F 491 
 TRP   0.012   0.002   TRP D 423 
 HIS   0.003   0.001   HIS D 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9978)
  covalent geometry    : angle       0.61426 (13548)
  SS BOND              : bond        0.00327 (   15)
  SS BOND              : angle       1.36814 (   30)
  hydrogen bonds       : bond        0.04507 (  330)
  hydrogen bonds       : angle       5.30994 (  891)

*********************** 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
  296 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 296
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 ASN cc_start: 0.8903 (m-40) cc_final: 0.8456 (m-40)
REVERT: B  314 LEU cc_start: 0.9114 (mt) cc_final: 0.8905 (mt)
REVERT: B  322 TYR cc_start: 0.7101 (t80) cc_final: 0.6049 (t80)
REVERT: B  335 ASP cc_start: 0.8338 (t0) cc_final: 0.8109 (t0)
REVERT: B  385 ASP cc_start: 0.6762 (t70) cc_final: 0.6320 (m-30)
REVERT: B  389 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7216 (mptt)
REVERT: B  411 LEU cc_start: 0.8248 (mp) cc_final: 0.7979 (mp)
REVERT: B  412 GLU cc_start: 0.8212 (tp30) cc_final: 0.7563 (tp30)
REVERT: B  487 MET cc_start: 0.5449 (tmm) cc_final: 0.5109 (tmm)
REVERT: C  142 LEU cc_start: 0.8736 (mt) cc_final: 0.8512 (mt)
REVERT: C  147 ILE cc_start: 0.8285 (mm) cc_final: 0.7961 (mm)
REVERT: C  176 LEU cc_start: 0.7707 (mt) cc_final: 0.7194 (tt)
REVERT: C  193 ASN cc_start: 0.8947 (m-40) cc_final: 0.8299 (m-40)
REVERT: D  275 GLU cc_start: 0.7089 (pt0) cc_final: 0.6788 (pm20)
REVERT: D  322 TYR cc_start: 0.7208 (t80) cc_final: 0.5427 (t80)
REVERT: D  335 ASP cc_start: 0.8443 (t0) cc_final: 0.8025 (t0)
REVERT: D  389 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7344 (mptt)
REVERT: D  436 TYR cc_start: 0.7272 (t80) cc_final: 0.6980 (t80)
REVERT: D  551 ASP cc_start: 0.6734 (m-30) cc_final: 0.6511 (t70)
REVERT: E  142 LEU cc_start: 0.8751 (mt) cc_final: 0.8522 (mt)
REVERT: E  147 ILE cc_start: 0.8538 (mm) cc_final: 0.8246 (mm)
REVERT: F  302 MET cc_start: 0.7403 (mmm) cc_final: 0.7045 (mmt)
REVERT: F  312 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7626 (tp-100)
REVERT: F  389 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7406 (mptt)
REVERT: F  430 TYR cc_start: 0.8395 (m-80) cc_final: 0.7779 (m-80)
REVERT: F  446 CYS cc_start: 0.4165 (t) cc_final: 0.3938 (t)
REVERT: F  463 MET cc_start: 0.6213 (ttm) cc_final: 0.5381 (ttm)
REVERT: F  487 MET cc_start: 0.5847 (tmm) cc_final: 0.5641 (tmm)
REVERT: F  551 ASP cc_start: 0.7209 (m-30) cc_final: 0.5992 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 296
  average time/residue: 0.0898
  time to fit residues: 38.2720
Evaluate side-chains
  241 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9980
   chunk 120 optimal weight:    9.9990
   chunk 119 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 19 optimal weight:    0.2980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
B 312 GLN
C 138 HIS
D 312 GLN
D 383 HIS
D 468 GLN
** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.158559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.135274 restraints weight = 20307.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.138804 restraints weight = 13203.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.141359 restraints weight = 9592.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.143179 restraints weight = 7505.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.144471 restraints weight = 6215.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9993  Z= 0.191
  Angle     :  0.697   8.122  13578  Z= 0.369
  Chirality :  0.048   0.255   1647
  Planarity :  0.005   0.041   1716
  Dihedral  :  6.147  32.716   1377
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.23), residues: 1281
  helix:  0.25 (0.29), residues: 327
  sheet: -2.31 (0.42), residues: 117
  loop : -1.72 (0.21), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 277 
 TYR   0.020   0.002   TYR D 424 
 PHE   0.014   0.002   PHE F 491 
 TRP   0.021   0.003   TRP D 423 
 HIS   0.004   0.001   HIS F 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9978)
  covalent geometry    : angle       0.69236 (13548)
  SS BOND              : bond        0.00567 (   15)
  SS BOND              : angle       1.80563 (   30)
  hydrogen bonds       : bond        0.05039 (  330)
  hydrogen bonds       : angle       5.74687 (  891)

*********************** 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  : 0.450 
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: A  176 LEU cc_start: 0.7664 (mt) cc_final: 0.7351 (tt)
REVERT: A  193 ASN cc_start: 0.9057 (m-40) cc_final: 0.8687 (m-40)
REVERT: B  322 TYR cc_start: 0.7572 (t80) cc_final: 0.5948 (t80)
REVERT: B  335 ASP cc_start: 0.8371 (t0) cc_final: 0.8037 (t0)
REVERT: B  389 LYS cc_start: 0.8503 (mmtt) cc_final: 0.7524 (mptt)
REVERT: B  463 MET cc_start: 0.7069 (ttm) cc_final: 0.6450 (ttm)
REVERT: B  487 MET cc_start: 0.5514 (tmm) cc_final: 0.5193 (tmm)
REVERT: C  142 LEU cc_start: 0.8946 (mt) cc_final: 0.8727 (mt)
REVERT: C  147 ILE cc_start: 0.8323 (mm) cc_final: 0.7971 (mm)
REVERT: C  193 ASN cc_start: 0.9011 (m-40) cc_final: 0.8345 (m-40)
REVERT: D  275 GLU cc_start: 0.7136 (pt0) cc_final: 0.6830 (pm20)
REVERT: D  322 TYR cc_start: 0.7562 (t80) cc_final: 0.5602 (t80)
REVERT: D  335 ASP cc_start: 0.8217 (t0) cc_final: 0.7822 (t0)
REVERT: D  340 GLU cc_start: 0.7203 (pm20) cc_final: 0.6991 (pm20)
REVERT: D  436 TYR cc_start: 0.7352 (t80) cc_final: 0.7050 (t80)
REVERT: D  463 MET cc_start: 0.6921 (ttm) cc_final: 0.6453 (ttm)
REVERT: D  487 MET cc_start: 0.5982 (tmm) cc_final: 0.5727 (tmm)
REVERT: E  142 LEU cc_start: 0.8924 (mt) cc_final: 0.8680 (mt)
REVERT: E  147 ILE cc_start: 0.8698 (mm) cc_final: 0.8350 (mm)
REVERT: F  305 MET cc_start: 0.2871 (mpp) cc_final: 0.2589 (mtm)
REVERT: F  312 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7915 (tp-100)
REVERT: F  389 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7716 (mptt)
REVERT: F  430 TYR cc_start: 0.8652 (m-80) cc_final: 0.8387 (m-80)
REVERT: F  458 ASN cc_start: 0.8107 (t0) cc_final: 0.7901 (t0)
REVERT: F  463 MET cc_start: 0.6621 (ttm) cc_final: 0.6319 (ttm)
REVERT: F  487 MET cc_start: 0.5701 (tmm) cc_final: 0.5373 (tmm)
REVERT: F  551 ASP cc_start: 0.7419 (m-30) cc_final: 0.6584 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.0849
  time to fit residues: 35.5850
Evaluate side-chains
  223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 35 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 117 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    0.4980
   chunk 49 optimal weight:   20.0000
   chunk 118 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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
C 209 ASN
D 312 GLN
D 468 GLN
E 138 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.161086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.138798 restraints weight = 20122.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.142252 restraints weight = 13135.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.144728 restraints weight = 9506.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.146547 restraints weight = 7439.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.147888 restraints weight = 6143.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9993  Z= 0.142
  Angle     :  0.649   9.670  13578  Z= 0.342
  Chirality :  0.047   0.245   1647
  Planarity :  0.004   0.044   1716
  Dihedral  :  5.870  27.618   1377
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.23), residues: 1281
  helix:  0.54 (0.28), residues: 321
  sheet: -2.13 (0.43), residues: 117
  loop : -1.71 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 277 
 TYR   0.014   0.001   TYR D 424 
 PHE   0.008   0.002   PHE D 491 
 TRP   0.016   0.002   TRP D 423 
 HIS   0.002   0.001   HIS B 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9978)
  covalent geometry    : angle       0.64421 (13548)
  SS BOND              : bond        0.00662 (   15)
  SS BOND              : angle       1.85228 (   30)
  hydrogen bonds       : bond        0.04556 (  330)
  hydrogen bonds       : angle       5.51470 (  891)

*********************** 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
  275 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8925 (mt) cc_final: 0.8711 (mt)
REVERT: A  193 ASN cc_start: 0.9041 (m-40) cc_final: 0.8725 (m-40)
REVERT: B  314 LEU cc_start: 0.9219 (mt) cc_final: 0.8997 (mt)
REVERT: B  322 TYR cc_start: 0.7406 (t80) cc_final: 0.6084 (t80)
REVERT: B  335 ASP cc_start: 0.8320 (t0) cc_final: 0.7958 (t0)
REVERT: B  389 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7499 (mptt)
REVERT: B  463 MET cc_start: 0.7064 (ttm) cc_final: 0.6841 (ttm)
REVERT: B  487 MET cc_start: 0.5563 (tmm) cc_final: 0.5248 (tmm)
REVERT: C  142 LEU cc_start: 0.8898 (mt) cc_final: 0.8694 (mt)
REVERT: C  193 ASN cc_start: 0.9071 (m-40) cc_final: 0.8430 (m-40)
REVERT: D  275 GLU cc_start: 0.7153 (pt0) cc_final: 0.6915 (pm20)
REVERT: D  322 TYR cc_start: 0.7477 (t80) cc_final: 0.5767 (t80)
REVERT: D  335 ASP cc_start: 0.8290 (t0) cc_final: 0.7814 (t0)
REVERT: D  340 GLU cc_start: 0.7143 (pm20) cc_final: 0.6938 (pm20)
REVERT: D  436 TYR cc_start: 0.7340 (t80) cc_final: 0.6990 (t80)
REVERT: D  463 MET cc_start: 0.6969 (ttm) cc_final: 0.6630 (ttm)
REVERT: D  487 MET cc_start: 0.5900 (tmm) cc_final: 0.5581 (tmm)
REVERT: D  508 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8116 (ttpt)
REVERT: D  551 ASP cc_start: 0.6891 (m-30) cc_final: 0.6425 (t70)
REVERT: E  142 LEU cc_start: 0.8917 (mt) cc_final: 0.8689 (mt)
REVERT: E  147 ILE cc_start: 0.8689 (mm) cc_final: 0.8314 (mm)
REVERT: F  305 MET cc_start: 0.2778 (mpp) cc_final: 0.2480 (mtm)
REVERT: F  312 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7867 (tp-100)
REVERT: F  389 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7658 (mptt)
REVERT: F  463 MET cc_start: 0.6683 (ttm) cc_final: 0.6404 (ttm)
REVERT: F  487 MET cc_start: 0.5736 (tmm) cc_final: 0.5393 (tmm)
REVERT: F  551 ASP cc_start: 0.7202 (m-30) cc_final: 0.5959 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 275
  average time/residue: 0.0851
  time to fit residues: 34.3330
Evaluate side-chains
  216 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 112 optimal weight:    0.9980
   chunk 37 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    3.5386

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.157261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.134715 restraints weight = 20620.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138010 restraints weight = 13754.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.140389 restraints weight = 10123.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.141907 restraints weight = 7967.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.143222 restraints weight = 6718.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9993  Z= 0.181
  Angle     :  0.699   7.438  13578  Z= 0.368
  Chirality :  0.048   0.279   1647
  Planarity :  0.004   0.043   1716
  Dihedral  :  6.078  27.081   1377
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.06 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.23), residues: 1281
  helix:  0.59 (0.29), residues: 333
  sheet: -1.96 (0.43), residues: 117
  loop : -1.71 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 277 
 TYR   0.020   0.002   TYR F 293 
 PHE   0.011   0.002   PHE D 329 
 TRP   0.023   0.003   TRP B 423 
 HIS   0.003   0.001   HIS E 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9978)
  covalent geometry    : angle       0.69471 (13548)
  SS BOND              : bond        0.00540 (   15)
  SS BOND              : angle       1.75967 (   30)
  hydrogen bonds       : bond        0.04795 (  330)
  hydrogen bonds       : angle       5.81887 (  891)

*********************** 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
  271 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 270
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  335 ASP cc_start: 0.8389 (t0) cc_final: 0.8015 (t0)
REVERT: B  385 ASP cc_start: 0.7555 (m-30) cc_final: 0.7123 (m-30)
REVERT: B  487 MET cc_start: 0.5509 (tmm) cc_final: 0.5298 (tmm)
REVERT: B  508 LYS cc_start: 0.8253 (ttpt) cc_final: 0.8020 (ttpt)
REVERT: B  567 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6369 (mm-30)
REVERT: C  147 ILE cc_start: 0.8250 (mm) cc_final: 0.7841 (mm)
REVERT: C  193 ASN cc_start: 0.9054 (m-40) cc_final: 0.8334 (m-40)
REVERT: D  275 GLU cc_start: 0.7131 (pt0) cc_final: 0.6927 (pm20)
REVERT: D  322 TYR cc_start: 0.7563 (t80) cc_final: 0.5756 (t80)
REVERT: D  335 ASP cc_start: 0.8282 (t0) cc_final: 0.7784 (t0)
REVERT: D  340 GLU cc_start: 0.7284 (pm20) cc_final: 0.7067 (pm20)
REVERT: D  436 TYR cc_start: 0.7355 (t80) cc_final: 0.6991 (t80)
REVERT: D  508 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8251 (tmmt)
REVERT: D  551 ASP cc_start: 0.6940 (m-30) cc_final: 0.6625 (t70)
REVERT: E  147 ILE cc_start: 0.8694 (mm) cc_final: 0.8337 (mm)
REVERT: F  305 MET cc_start: 0.2990 (mpp) cc_final: 0.2569 (mtm)
REVERT: F  335 ASP cc_start: 0.8475 (t0) cc_final: 0.8202 (t0)
REVERT: F  430 TYR cc_start: 0.8788 (m-80) cc_final: 0.8521 (m-80)
REVERT: F  487 MET cc_start: 0.5965 (tmm) cc_final: 0.5385 (tmm)
REVERT: F  551 ASP cc_start: 0.7348 (m-30) cc_final: 0.6549 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 270
  average time/residue: 0.0782
  time to fit residues: 31.6519
Evaluate side-chains
  218 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 97 optimal weight:    0.3980
   chunk 111 optimal weight:    0.0170
   chunk 105 optimal weight:    2.9990
   chunk 91 optimal weight:   20.0000
   chunk 17 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 119 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.0222

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
E 138 HIS
F 312 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.164285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.142823 restraints weight = 19991.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.146097 restraints weight = 13442.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.148357 restraints weight = 9873.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.150097 restraints weight = 7786.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.151302 restraints weight = 6467.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9993  Z= 0.116
  Angle     :  0.638   7.726  13578  Z= 0.331
  Chirality :  0.047   0.297   1647
  Planarity :  0.004   0.044   1716
  Dihedral  :  5.656  23.753   1377
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.23), residues: 1281
  helix:  0.55 (0.28), residues: 339
  sheet: -1.71 (0.45), residues: 117
  loop : -1.71 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 334 
 TYR   0.011   0.001   TYR D 293 
 PHE   0.011   0.002   PHE B 441 
 TRP   0.012   0.002   TRP B 423 
 HIS   0.004   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9978)
  covalent geometry    : angle       0.63405 (13548)
  SS BOND              : bond        0.00423 (   15)
  SS BOND              : angle       1.58077 (   30)
  hydrogen bonds       : bond        0.04112 (  330)
  hydrogen bonds       : angle       5.38289 (  891)

*********************** 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
  291 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  314 LEU cc_start: 0.9232 (mt) cc_final: 0.9010 (mt)
REVERT: B  322 TYR cc_start: 0.7151 (t80) cc_final: 0.6047 (t80)
REVERT: B  335 ASP cc_start: 0.8320 (t0) cc_final: 0.7908 (t0)
REVERT: B  385 ASP cc_start: 0.7272 (m-30) cc_final: 0.6939 (m-30)
REVERT: B  463 MET cc_start: 0.7022 (mtt) cc_final: 0.6144 (mtt)
REVERT: B  487 MET cc_start: 0.5513 (tmm) cc_final: 0.5278 (tmm)
REVERT: B  567 GLU cc_start: 0.6255 (mm-30) cc_final: 0.5948 (mm-30)
REVERT: C  193 ASN cc_start: 0.9020 (m-40) cc_final: 0.8448 (m-40)
REVERT: D  275 GLU cc_start: 0.6832 (pt0) cc_final: 0.6626 (pm20)
REVERT: D  322 TYR cc_start: 0.7359 (t80) cc_final: 0.5739 (t80)
REVERT: D  335 ASP cc_start: 0.8235 (t0) cc_final: 0.7649 (t0)
REVERT: D  340 GLU cc_start: 0.7265 (pm20) cc_final: 0.7055 (pm20)
REVERT: D  436 TYR cc_start: 0.7370 (t80) cc_final: 0.7047 (t80)
REVERT: D  487 MET cc_start: 0.6183 (tmm) cc_final: 0.5919 (tmm)
REVERT: D  510 TYR cc_start: 0.7202 (t80) cc_final: 0.6786 (t80)
REVERT: D  551 ASP cc_start: 0.6750 (m-30) cc_final: 0.6091 (t70)
REVERT: E  142 LEU cc_start: 0.8818 (mt) cc_final: 0.8557 (mt)
REVERT: F  335 ASP cc_start: 0.8464 (t0) cc_final: 0.8161 (t0)
REVERT: F  385 ASP cc_start: 0.7219 (m-30) cc_final: 0.6953 (m-30)
REVERT: F  487 MET cc_start: 0.5917 (tmm) cc_final: 0.5412 (tmm)
REVERT: F  551 ASP cc_start: 0.7345 (m-30) cc_final: 0.6132 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.0823
  time to fit residues: 34.8283
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  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 123 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0470
   chunk 35 optimal weight:   40.0000
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 82 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0980
   overall best weight:    0.4680

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

Flipped N/Q/H residues before XYZ refinement:
B 344 GLN
** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 574 ASN
C 209 ASN
D 574 ASN
E 138 HIS
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 574 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.166155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.143749 restraints weight = 19810.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.147213 restraints weight = 12960.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.149756 restraints weight = 9390.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.151539 restraints weight = 7306.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152935 restraints weight = 6014.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.5265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9993  Z= 0.110
  Angle     :  0.625   7.555  13578  Z= 0.324
  Chirality :  0.047   0.287   1647
  Planarity :  0.004   0.040   1716
  Dihedral  :  5.427  21.941   1377
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.23), residues: 1281
  helix:  0.69 (0.28), residues: 333
  sheet: -1.51 (0.46), residues: 117
  loop : -1.53 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 277 
 TYR   0.015   0.001   TYR D 321 
 PHE   0.022   0.002   PHE D 491 
 TRP   0.012   0.001   TRP B 423 
 HIS   0.002   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9978)
  covalent geometry    : angle       0.62190 (13548)
  SS BOND              : bond        0.00341 (   15)
  SS BOND              : angle       1.50621 (   30)
  hydrogen bonds       : bond        0.03952 (  330)
  hydrogen bonds       : angle       5.14689 (  891)

*********************** 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
  293 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 THR cc_start: 0.7478 (p) cc_final: 0.7094 (p)
REVERT: B  314 LEU cc_start: 0.9205 (mt) cc_final: 0.8998 (mt)
REVERT: B  322 TYR cc_start: 0.7127 (t80) cc_final: 0.6034 (t80)
REVERT: B  335 ASP cc_start: 0.8290 (t0) cc_final: 0.7976 (t0)
REVERT: B  408 VAL cc_start: 0.8210 (t) cc_final: 0.7979 (t)
REVERT: B  487 MET cc_start: 0.5423 (tmm) cc_final: 0.5188 (tmm)
REVERT: B  527 ILE cc_start: 0.8262 (mp) cc_final: 0.8015 (mt)
REVERT: B  567 GLU cc_start: 0.6195 (mm-30) cc_final: 0.5952 (mm-30)
REVERT: C  193 ASN cc_start: 0.8993 (m-40) cc_final: 0.8419 (m-40)
REVERT: D  314 LEU cc_start: 0.9188 (mt) cc_final: 0.8978 (mt)
REVERT: D  322 TYR cc_start: 0.7326 (t80) cc_final: 0.6320 (t80)
REVERT: D  335 ASP cc_start: 0.8235 (t0) cc_final: 0.7608 (t0)
REVERT: D  340 GLU cc_start: 0.7372 (pm20) cc_final: 0.7018 (pm20)
REVERT: D  371 ILE cc_start: 0.8421 (mm) cc_final: 0.8072 (mp)
REVERT: D  436 TYR cc_start: 0.7487 (t80) cc_final: 0.7200 (t80)
REVERT: D  487 MET cc_start: 0.6144 (tmm) cc_final: 0.5811 (tmm)
REVERT: D  510 TYR cc_start: 0.7417 (t80) cc_final: 0.6965 (t80)
REVERT: D  551 ASP cc_start: 0.6625 (m-30) cc_final: 0.6156 (t70)
REVERT: E  142 LEU cc_start: 0.8819 (mt) cc_final: 0.8581 (mt)
REVERT: F  308 GLU cc_start: 0.5519 (mp0) cc_final: 0.5190 (mp0)
REVERT: F  314 LEU cc_start: 0.9083 (mt) cc_final: 0.8876 (mt)
REVERT: F  335 ASP cc_start: 0.8493 (t0) cc_final: 0.8049 (t0)
REVERT: F  463 MET cc_start: 0.7135 (ttm) cc_final: 0.6440 (ttm)
REVERT: F  487 MET cc_start: 0.5765 (tmm) cc_final: 0.5319 (tmm)
REVERT: F  551 ASP cc_start: 0.7239 (m-30) cc_final: 0.6221 (t70)
REVERT: F  570 ASP cc_start: 0.7836 (m-30) cc_final: 0.7398 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.0792
  time to fit residues: 34.3014
Evaluate side-chains
  231 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    9.9990
   chunk 95 optimal weight:    0.4980
   chunk 114 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
B 344 GLN
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 409 HIS
** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.162215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.139606 restraints weight = 20029.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.143003 restraints weight = 13223.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.145427 restraints weight = 9641.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.147211 restraints weight = 7561.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.148377 restraints weight = 6258.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.5291

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= 0.145
  Angle     :  0.678  10.019  13578  Z= 0.348
  Chirality :  0.048   0.305   1647
  Planarity :  0.004   0.037   1716
  Dihedral  :  5.638  26.000   1377
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.90 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.23), residues: 1281
  helix:  0.53 (0.28), residues: 351
  sheet: -1.50 (0.45), residues: 117
  loop : -1.59 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 277 
 TYR   0.016   0.002   TYR F 293 
 PHE   0.024   0.002   PHE D 491 
 TRP   0.019   0.003   TRP D 423 
 HIS   0.002   0.001   HIS D 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9978)
  covalent geometry    : angle       0.67390 (13548)
  SS BOND              : bond        0.00620 (   15)
  SS BOND              : angle       1.75471 (   30)
  hydrogen bonds       : bond        0.04321 (  330)
  hydrogen bonds       : angle       5.26065 (  891)

*********************** 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: 1
    poor density    : 284
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8875 (mt) cc_final: 0.8650 (mt)
REVERT: A  204 THR cc_start: 0.7537 (p) cc_final: 0.7250 (p)
REVERT: B  322 TYR cc_start: 0.7353 (t80) cc_final: 0.5932 (t80)
REVERT: B  335 ASP cc_start: 0.8311 (t0) cc_final: 0.7977 (t0)
REVERT: B  385 ASP cc_start: 0.7065 (m-30) cc_final: 0.6823 (m-30)
REVERT: B  463 MET cc_start: 0.6996 (ttm) cc_final: 0.6727 (ttm)
REVERT: B  487 MET cc_start: 0.5484 (tmm) cc_final: 0.5246 (tmm)
REVERT: B  567 GLU cc_start: 0.6338 (mm-30) cc_final: 0.5949 (mm-30)
REVERT: C  193 ASN cc_start: 0.9021 (m-40) cc_final: 0.8416 (m-40)
REVERT: D  322 TYR cc_start: 0.7714 (t80) cc_final: 0.6229 (t80)
REVERT: D  335 ASP cc_start: 0.8213 (t0) cc_final: 0.7629 (t0)
REVERT: D  340 GLU cc_start: 0.7330 (pm20) cc_final: 0.7056 (pm20)
REVERT: D  371 ILE cc_start: 0.8581 (mm) cc_final: 0.8221 (mp)
REVERT: D  436 TYR cc_start: 0.7437 (t80) cc_final: 0.7181 (t80)
REVERT: D  487 MET cc_start: 0.5905 (tmm) cc_final: 0.4225 (mtm)
REVERT: D  510 TYR cc_start: 0.7257 (t80) cc_final: 0.6977 (t80)
REVERT: D  551 ASP cc_start: 0.6819 (m-30) cc_final: 0.6164 (t70)
REVERT: E  142 LEU cc_start: 0.8835 (mt) cc_final: 0.8632 (mt)
REVERT: F  308 GLU cc_start: 0.5500 (mp0) cc_final: 0.5173 (mp0)
REVERT: F  335 ASP cc_start: 0.8534 (t0) cc_final: 0.8028 (t0)
REVERT: F  463 MET cc_start: 0.6996 (ttm) cc_final: 0.6688 (ttm)
REVERT: F  487 MET cc_start: 0.5926 (tmm) cc_final: 0.5394 (tmm)
REVERT: F  551 ASP cc_start: 0.7319 (m-30) cc_final: 0.6201 (t70)
REVERT: F  570 ASP cc_start: 0.7760 (m-30) cc_final: 0.7327 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 285
  average time/residue: 0.0873
  time to fit residues: 36.2375
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  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 105 optimal weight:    0.0770
   chunk 120 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 102 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 89 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 79 optimal weight:    9.9990
   chunk 118 optimal weight:    8.9990
   overall best weight:    1.3520

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
A 209 ASN
B 257 GLN
E 138 HIS
E 200 ASN
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.164478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.141813 restraints weight = 20028.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.145095 restraints weight = 13273.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.147554 restraints weight = 9783.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.149226 restraints weight = 7717.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.150618 restraints weight = 6441.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.5450

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= 0.124
  Angle     :  0.680   9.051  13578  Z= 0.352
  Chirality :  0.049   0.327   1647
  Planarity :  0.004   0.040   1716
  Dihedral  :  5.558  24.773   1377
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.23), residues: 1281
  helix:  0.81 (0.29), residues: 330
  sheet: -1.32 (0.47), residues: 117
  loop : -1.46 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 277 
 TYR   0.012   0.001   TYR B 321 
 PHE   0.014   0.002   PHE D 491 
 TRP   0.015   0.002   TRP B 423 
 HIS   0.002   0.000   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9978)
  covalent geometry    : angle       0.67510 (13548)
  SS BOND              : bond        0.00426 (   15)
  SS BOND              : angle       1.77840 (   30)
  hydrogen bonds       : bond        0.04240 (  330)
  hydrogen bonds       : angle       5.23617 (  891)

********************** 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
  274 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8839 (mt) cc_final: 0.8614 (mt)
REVERT: A  204 THR cc_start: 0.7539 (p) cc_final: 0.7170 (p)
REVERT: B  322 TYR cc_start: 0.7287 (t80) cc_final: 0.6048 (t80)
REVERT: B  326 LEU cc_start: 0.8042 (tp) cc_final: 0.7785 (tt)
REVERT: B  335 ASP cc_start: 0.8260 (t0) cc_final: 0.7945 (t0)
REVERT: B  463 MET cc_start: 0.7102 (ttm) cc_final: 0.6812 (ttm)
REVERT: B  487 MET cc_start: 0.5539 (tmm) cc_final: 0.5255 (tmm)
REVERT: B  527 ILE cc_start: 0.8291 (mp) cc_final: 0.8061 (mt)
REVERT: B  532 CYS cc_start: 0.4575 (p) cc_final: 0.4366 (t)
REVERT: B  567 GLU cc_start: 0.6253 (mm-30) cc_final: 0.5938 (mm-30)
REVERT: D  322 TYR cc_start: 0.7647 (t80) cc_final: 0.6064 (t80)
REVERT: D  335 ASP cc_start: 0.8221 (t0) cc_final: 0.7642 (t0)
REVERT: D  340 GLU cc_start: 0.7410 (pm20) cc_final: 0.7055 (pm20)
REVERT: D  371 ILE cc_start: 0.8484 (mm) cc_final: 0.8218 (mp)
REVERT: D  436 TYR cc_start: 0.7442 (t80) cc_final: 0.7106 (t80)
REVERT: D  551 ASP cc_start: 0.6760 (m-30) cc_final: 0.6232 (t70)
REVERT: E  142 LEU cc_start: 0.8793 (mt) cc_final: 0.8589 (mt)
REVERT: F  308 GLU cc_start: 0.5491 (mp0) cc_final: 0.5151 (mp0)
REVERT: F  314 LEU cc_start: 0.9149 (mt) cc_final: 0.8940 (mt)
REVERT: F  335 ASP cc_start: 0.8446 (t0) cc_final: 0.8037 (t0)
REVERT: F  371 ILE cc_start: 0.8472 (mm) cc_final: 0.8175 (mp)
REVERT: F  463 MET cc_start: 0.6966 (ttm) cc_final: 0.6746 (ttm)
REVERT: F  468 GLN cc_start: 0.8377 (mm110) cc_final: 0.7081 (mm-40)
REVERT: F  487 MET cc_start: 0.5889 (tmm) cc_final: 0.5435 (tmm)
REVERT: F  551 ASP cc_start: 0.7290 (m-30) cc_final: 0.6229 (t70)
REVERT: F  570 ASP cc_start: 0.7480 (m-30) cc_final: 0.6973 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.0817
  time to fit residues: 33.0414
Evaluate side-chains
  230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 121 optimal weight:    0.0970
   chunk 52 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0470
   chunk 36 optimal weight:   20.0000
   chunk 102 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    3.0282

-------------------------------------------------------------------------------
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 193 ASN
D 468 GLN
E 138 HIS
** E 200 ASN ** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.160300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.137532 restraints weight = 20108.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140860 restraints weight = 13356.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.143249 restraints weight = 9806.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.145011 restraints weight = 7728.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.145932 restraints weight = 6409.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.5471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9993  Z= 0.166
  Angle     :  0.722   9.250  13578  Z= 0.375
  Chirality :  0.049   0.332   1647
  Planarity :  0.004   0.037   1716
  Dihedral  :  5.792  24.648   1377
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.23), residues: 1281
  helix:  0.44 (0.28), residues: 351
  sheet: -1.30 (0.46), residues: 117
  loop : -1.64 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 277 
 TYR   0.020   0.002   TYR F 293 
 PHE   0.011   0.002   PHE F 526 
 TRP   0.022   0.003   TRP D 423 
 HIS   0.002   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9978)
  covalent geometry    : angle       0.71623 (13548)
  SS BOND              : bond        0.00563 (   15)
  SS BOND              : angle       1.99221 (   30)
  hydrogen bonds       : bond        0.04687 (  330)
  hydrogen bonds       : angle       5.56777 (  891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1534.09 seconds
wall clock time: 27 minutes 21.96 seconds (1641.96 seconds total)