Starting phenix.real_space_refine
on Fri Mar 14 05:52:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xye_10649/03_2025/6xye_10649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xye_10649/03_2025/6xye_10649.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2025/6xye_10649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2025/6xye_10649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2025/6xye_10649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xye_10649/03_2025/6xye_10649.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    6219      2.51       5
     N    1656      2.21       5
     O    1902      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9834
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 588
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "B"
      Number of atoms: 2690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2690
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 13, 'TRANS': 343}
  Restraints were copied for chains:
    D, F, C, E
  Time building chain proxies: 5.64, per 1000 atoms: 0.57
  Number of scatterers: 9834
  At special positions: 0
  Unit cell: (102.1, 106.184, 101.079, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1902      8.00
     N    1656      7.00
     C    6219      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 24 sheets defined
      29.2% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 139 through 142
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 182 through 207
      removed outlier: 3.689A  pdb=" N   LYS A 190 " --> pdb=" O   GLY A 186 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
      Proline residue:  A 198  - end of helix
    Processing helix  chain 'B' and resid 232 through 235
      No H-bonds generated for 'chain 'B' and resid 232 through 235'
    Processing helix  chain 'B' and resid 240 through 251
    Processing helix  chain 'B' and resid 260 through 268
      removed outlier: 3.670A  pdb=" N   GLU B 267 " --> pdb=" O   ARG B 263 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   GLN B 268 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 307 through 328
    Processing helix  chain 'B' and resid 355 through 360
    Processing helix  chain 'B' and resid 368 through 372
    Processing helix  chain 'B' and resid 465 through 473
      removed outlier: 5.344A  pdb=" N   CYS B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG B 472 " --> pdb=" O   GLN B 468 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY B 473 " --> pdb=" O   GLN B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 582
    Processing helix  chain 'C' and resid 139 through 142
    Processing helix  chain 'C' and resid 175 through 177
      No H-bonds generated for 'chain 'C' and resid 175 through 177'
    Processing helix  chain 'C' and resid 182 through 207
      removed outlier: 3.690A  pdb=" N   LYS C 190 " --> pdb=" O   GLY C 186 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN C 193 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER C 194 " --> pdb=" O   LYS C 190 " (cutoff:3.500A)
      Proline residue:  C 198  - end of helix
    Processing helix  chain 'D' and resid 232 through 235
      No H-bonds generated for 'chain 'D' and resid 232 through 235'
    Processing helix  chain 'D' and resid 240 through 251
    Processing helix  chain 'D' and resid 260 through 268
      removed outlier: 3.670A  pdb=" N   GLU D 267 " --> pdb=" O   ARG D 263 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   GLN D 268 " --> pdb=" O   THR D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 296
    Processing helix  chain 'D' and resid 300 through 304
    Processing helix  chain 'D' and resid 307 through 328
    Processing helix  chain 'D' and resid 355 through 360
    Processing helix  chain 'D' and resid 368 through 372
    Processing helix  chain 'D' and resid 465 through 473
      removed outlier: 5.344A  pdb=" N   CYS D 470 " --> pdb=" O   LEU D 466 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE D 471 " --> pdb=" O   LEU D 467 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG D 472 " --> pdb=" O   GLN D 468 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY D 473 " --> pdb=" O   GLN D 469 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 568 through 582
    Processing helix  chain 'E' and resid 139 through 142
    Processing helix  chain 'E' and resid 175 through 177
      No H-bonds generated for 'chain 'E' and resid 175 through 177'
    Processing helix  chain 'E' and resid 182 through 207
      removed outlier: 3.689A  pdb=" N   LYS E 190 " --> pdb=" O   GLY E 186 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN E 193 " --> pdb=" O   GLU E 189 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER E 194 " --> pdb=" O   LYS E 190 " (cutoff:3.500A)
      Proline residue:  E 198  - end of helix
    Processing helix  chain 'F' and resid 232 through 235
      No H-bonds generated for 'chain 'F' and resid 232 through 235'
    Processing helix  chain 'F' and resid 240 through 251
    Processing helix  chain 'F' and resid 260 through 268
      removed outlier: 3.670A  pdb=" N   GLU F 267 " --> pdb=" O   ARG F 263 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLN F 268 " --> pdb=" O   THR F 264 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 291 through 296
    Processing helix  chain 'F' and resid 300 through 304
    Processing helix  chain 'F' and resid 307 through 328
    Processing helix  chain 'F' and resid 355 through 360
    Processing helix  chain 'F' and resid 368 through 372
    Processing helix  chain 'F' and resid 465 through 473
      removed outlier: 5.343A  pdb=" N   CYS F 470 " --> pdb=" O   LEU F 466 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE F 471 " --> pdb=" O   LEU F 467 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG F 472 " --> pdb=" O   GLN F 468 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY F 473 " --> pdb=" O   GLN F 469 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 568 through 582
    Processing sheet with id=A, first strand: chain 'B' and resid 446 through 448
      removed outlier: 7.862A  pdb=" N   ALA B 453 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   HIS A 154 " --> pdb=" O   ALA B 453 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   CYS B 455 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LYS A 156 " --> pdb=" O   CYS B 455 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ASP A 151 " --> pdb=" O   ARG B 410 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 155 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   VAL B 406 " --> pdb=" O   TYR A 155 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 156 through 159
    Processing sheet with id=C, first strand: chain 'A' and resid 163 through 169
      removed outlier: 6.275A  pdb=" N   SER B 394 " --> pdb=" O   ILE B 381 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE B 381 " --> pdb=" O   SER B 394 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   SER B 396 " --> pdb=" O   THR B 379 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   THR B 379 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'B' and resid 273 through 276
      removed outlier: 6.190A  pdb=" N   ILE B 273 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL B 287 " --> pdb=" O   ILE B 273 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU B 275 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B 285 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=D
    Processing sheet with id=E, first strand: chain 'B' and resid 416 through 418
    Processing sheet with id=F, first strand: chain 'B' and resid 424 through 425
    Processing sheet with id=G, first strand: chain 'B' and resid 491 through 494
    Processing sheet with id=H, first strand: chain 'B' and resid 507 through 509
    Processing sheet with id=I, first strand: chain 'D' and resid 446 through 448
      removed outlier: 7.861A  pdb=" N   ALA D 453 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   HIS C 154 " --> pdb=" O   ALA D 453 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   CYS D 455 " --> pdb=" O   HIS C 154 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LYS C 156 " --> pdb=" O   CYS D 455 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP C 151 " --> pdb=" O   ARG D 410 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR C 155 " --> pdb=" O   VAL D 406 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   VAL D 406 " --> pdb=" O   TYR C 155 " (cutoff:3.500A)
    Processing sheet with id=J, first strand: chain 'C' and resid 156 through 159
    Processing sheet with id=K, first strand: chain 'C' and resid 163 through 169
      removed outlier: 6.275A  pdb=" N   SER D 394 " --> pdb=" O   ILE D 381 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE D 381 " --> pdb=" O   SER D 394 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   SER D 396 " --> pdb=" O   THR D 379 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   THR D 379 " --> pdb=" O   SER D 396 " (cutoff:3.500A)
    Processing sheet with id=L, first strand: chain 'D' and resid 273 through 276
      removed outlier: 6.190A  pdb=" N   ILE D 273 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL D 287 " --> pdb=" O   ILE D 273 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU D 275 " --> pdb=" O   ILE D 285 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE D 285 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=L
    Processing sheet with id=M, first strand: chain 'D' and resid 416 through 418
    Processing sheet with id=N, first strand: chain 'D' and resid 424 through 425
    Processing sheet with id=O, first strand: chain 'D' and resid 491 through 494
    Processing sheet with id=P, first strand: chain 'D' and resid 507 through 509
    Processing sheet with id=Q, first strand: chain 'F' and resid 446 through 448
      removed outlier: 7.862A  pdb=" N   ALA F 453 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   HIS E 154 " --> pdb=" O   ALA F 453 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   CYS F 455 " --> pdb=" O   HIS E 154 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LYS E 156 " --> pdb=" O   CYS F 455 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ASP E 151 " --> pdb=" O   ARG F 410 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR E 155 " --> pdb=" O   VAL F 406 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   VAL F 406 " --> pdb=" O   TYR E 155 " (cutoff:3.500A)
    Processing sheet with id=R, first strand: chain 'E' and resid 156 through 159
    Processing sheet with id=S, first strand: chain 'E' and resid 163 through 169
      removed outlier: 6.276A  pdb=" N   SER F 394 " --> pdb=" O   ILE F 381 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE F 381 " --> pdb=" O   SER F 394 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   SER F 396 " --> pdb=" O   THR F 379 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   THR F 379 " --> pdb=" O   SER F 396 " (cutoff:3.500A)
    Processing sheet with id=T, first strand: chain 'F' and resid 273 through 276
      removed outlier: 6.190A  pdb=" N   ILE F 273 " --> pdb=" O   VAL F 287 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL F 287 " --> pdb=" O   ILE F 273 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLU F 275 " --> pdb=" O   ILE F 285 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE F 285 " --> pdb=" O   GLU F 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=T
    Processing sheet with id=U, first strand: chain 'F' and resid 416 through 418
    Processing sheet with id=V, first strand: chain 'F' and resid 424 through 425
    Processing sheet with id=W, first strand: chain 'F' and resid 491 through 494
    Processing sheet with id=X, first strand: chain 'F' and resid 507 through 509

    330 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.81

  Time building geometry restraints manager: 2.82 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.890
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.970
-------------------------------------------------------------------------------
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   9978  Z= 0.664
  Angle     :  1.295   7.767  13548  Z= 0.911
  Chirality :  0.087   0.288   1647
  Planarity :  0.007   0.042   1716
  Dihedral  : 10.029  74.225   3687
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.21), residues: 1281
  helix: -1.87 (0.25), residues: 342
  sheet: -3.21 (0.41), residues: 105
  loop : -2.05 (0.20), residues: 834

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

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

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 380
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8999 (mt) cc_final: 0.8697 (mt)
REVERT: A  173 ASN cc_start: 0.7386 (t0) cc_final: 0.7112 (t0)
REVERT: A  193 ASN cc_start: 0.8737 (m-40) cc_final: 0.8248 (m-40)
REVERT: B  322 TYR cc_start: 0.7309 (t80) cc_final: 0.5901 (t80)
REVERT: B  385 ASP cc_start: 0.6926 (t70) cc_final: 0.6679 (m-30)
REVERT: B  389 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7389 (mptt)
REVERT: B  411 LEU cc_start: 0.8406 (mt) cc_final: 0.8122 (mp)
REVERT: B  412 GLU cc_start: 0.8062 (tp30) cc_final: 0.7503 (tp30)
REVERT: B  460 LEU cc_start: 0.9090 (mt) cc_final: 0.8781 (tt)
REVERT: B  463 MET cc_start: 0.6900 (ttm) cc_final: 0.5346 (ttm)
REVERT: C  142 LEU cc_start: 0.9009 (mt) cc_final: 0.8708 (mt)
REVERT: C  173 ASN cc_start: 0.7560 (t0) cc_final: 0.7325 (t0)
REVERT: C  193 ASN cc_start: 0.8798 (m-40) cc_final: 0.8162 (m-40)
REVERT: D  389 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7525 (mptt)
REVERT: D  436 TYR cc_start: 0.6971 (t80) cc_final: 0.6659 (t80)
REVERT: D  463 MET cc_start: 0.6952 (ttm) cc_final: 0.5710 (ttm)
REVERT: D  551 ASP cc_start: 0.7378 (m-30) cc_final: 0.6743 (t70)
REVERT: D  580 LYS cc_start: 0.9178 (tttt) cc_final: 0.8485 (mttm)
REVERT: E  142 LEU cc_start: 0.9012 (mt) cc_final: 0.8709 (mt)
REVERT: E  173 ASN cc_start: 0.7548 (t0) cc_final: 0.7313 (t0)
REVERT: E  193 ASN cc_start: 0.8685 (m-40) cc_final: 0.8469 (m-40)
REVERT: F  276 ILE cc_start: 0.8922 (mm) cc_final: 0.8709 (pt)
REVERT: F  302 MET cc_start: 0.7249 (mmm) cc_final: 0.6951 (mmt)
REVERT: F  389 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7583 (mptt)
REVERT: F  422 GLU cc_start: 0.6669 (tt0) cc_final: 0.6319 (mp0)
REVERT: F  430 TYR cc_start: 0.8339 (m-80) cc_final: 0.8056 (m-80)
REVERT: F  436 TYR cc_start: 0.7039 (t80) cc_final: 0.6799 (t80)
REVERT: F  463 MET cc_start: 0.6671 (ttm) cc_final: 0.5420 (ttm)
REVERT: F  510 TYR cc_start: 0.7011 (t80) cc_final: 0.6364 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 380
  average time/residue: 0.2428
  time to fit residues: 124.8103
Evaluate side-chains
  251 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0270
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 98 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0770
   chunk 60 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 114 optimal weight:    7.9990
   overall best weight:    1.3600

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

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

Total number of N/Q/H flips: 19

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9978  Z= 0.202
  Angle     :  0.671   7.700  13548  Z= 0.354
  Chirality :  0.047   0.330   1647
  Planarity :  0.004   0.035   1716
  Dihedral  :  6.436  36.307   1377
  Min Nonbonded Distance : 2.561

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.22), residues: 1281
  helix: -0.53 (0.26), residues: 360
  sheet: -2.59 (0.43), residues: 105
  loop : -1.73 (0.21), residues: 816

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

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

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8856 (mt) cc_final: 0.8578 (mt)
REVERT: A  147 ILE cc_start: 0.8458 (mm) cc_final: 0.8215 (mm)
REVERT: A  193 ASN cc_start: 0.8890 (m-40) cc_final: 0.8424 (m-40)
REVERT: B  293 TYR cc_start: 0.5202 (t80) cc_final: 0.4913 (t80)
REVERT: B  322 TYR cc_start: 0.7284 (t80) cc_final: 0.6040 (t80)
REVERT: B  385 ASP cc_start: 0.6727 (t70) cc_final: 0.6425 (m-30)
REVERT: B  389 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7261 (mptt)
REVERT: B  408 VAL cc_start: 0.8399 (t) cc_final: 0.8168 (t)
REVERT: B  411 LEU cc_start: 0.8388 (mt) cc_final: 0.8171 (mp)
REVERT: B  412 GLU cc_start: 0.8260 (tp30) cc_final: 0.7545 (tp30)
REVERT: B  463 MET cc_start: 0.6591 (ttm) cc_final: 0.6358 (ttm)
REVERT: B  487 MET cc_start: 0.5594 (tmm) cc_final: 0.5389 (tmm)
REVERT: B  551 ASP cc_start: 0.7320 (m-30) cc_final: 0.6769 (t70)
REVERT: C  142 LEU cc_start: 0.8813 (mt) cc_final: 0.8599 (mt)
REVERT: C  147 ILE cc_start: 0.8299 (mm) cc_final: 0.7995 (mm)
REVERT: C  176 LEU cc_start: 0.7773 (mt) cc_final: 0.7170 (tt)
REVERT: C  193 ASN cc_start: 0.8937 (m-40) cc_final: 0.8400 (m-40)
REVERT: D  275 GLU cc_start: 0.7174 (pt0) cc_final: 0.6764 (pm20)
REVERT: D  389 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7451 (mptt)
REVERT: D  436 TYR cc_start: 0.7409 (t80) cc_final: 0.6998 (t80)
REVERT: D  551 ASP cc_start: 0.7164 (m-30) cc_final: 0.6635 (t70)
REVERT: E  142 LEU cc_start: 0.8763 (mt) cc_final: 0.8523 (mt)
REVERT: E  147 ILE cc_start: 0.8486 (mm) cc_final: 0.8239 (mm)
REVERT: F  275 GLU cc_start: 0.7050 (pt0) cc_final: 0.6841 (pm20)
REVERT: F  302 MET cc_start: 0.7357 (mmm) cc_final: 0.7069 (mmt)
REVERT: F  312 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7728 (tp-100)
REVERT: F  314 LEU cc_start: 0.9225 (mt) cc_final: 0.9014 (mt)
REVERT: F  322 TYR cc_start: 0.7500 (t80) cc_final: 0.7290 (t80)
REVERT: F  385 ASP cc_start: 0.8041 (m-30) cc_final: 0.7678 (m-30)
REVERT: F  389 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7593 (mptt)
REVERT: F  430 TYR cc_start: 0.8291 (m-80) cc_final: 0.7678 (m-80)
REVERT: F  487 MET cc_start: 0.5550 (tmm) cc_final: 0.5329 (tmm)
REVERT: F  508 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7721 (mtmm)
REVERT: F  510 TYR cc_start: 0.6803 (t80) cc_final: 0.6347 (t80)
REVERT: F  551 ASP cc_start: 0.7577 (m-30) cc_final: 0.6312 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 305
  average time/residue: 0.2074
  time to fit residues: 89.8246
Evaluate side-chains
  242 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 35 optimal weight:   20.0000
   chunk 4 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0970
   chunk 91 optimal weight:    0.0020
   chunk 114 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.0388

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.166055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.144008 restraints weight = 19509.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.147441 restraints weight = 12781.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.150003 restraints weight = 9279.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9978  Z= 0.167
  Angle     :  0.604   6.208  13548  Z= 0.321
  Chirality :  0.046   0.220   1647
  Planarity :  0.004   0.039   1716
  Dihedral  :  5.840  27.536   1377
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.22), residues: 1281
  helix:  0.01 (0.27), residues: 342
  sheet: -2.05 (0.53), residues: 87
  loop : -1.76 (0.20), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 423 
 HIS   0.003   0.001   HIS D 250 
 PHE   0.009   0.002   PHE F 441 
 TYR   0.013   0.001   TYR D 424 
 ARG   0.006   0.001   ARG D 547 

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

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8802 (mt) cc_final: 0.8598 (mt)
REVERT: A  176 LEU cc_start: 0.7543 (mt) cc_final: 0.7323 (tt)
REVERT: A  193 ASN cc_start: 0.8882 (m-40) cc_final: 0.8452 (m-40)
REVERT: B  250 HIS cc_start: 0.6241 (t70) cc_final: 0.5918 (t70)
REVERT: B  312 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7689 (tp-100)
REVERT: B  322 TYR cc_start: 0.7143 (t80) cc_final: 0.6024 (t80)
REVERT: B  335 ASP cc_start: 0.8353 (t0) cc_final: 0.8120 (t0)
REVERT: B  385 ASP cc_start: 0.6838 (t70) cc_final: 0.6315 (m-30)
REVERT: B  389 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7196 (mptt)
REVERT: B  487 MET cc_start: 0.5393 (tmm) cc_final: 0.5087 (tmm)
REVERT: C  142 LEU cc_start: 0.8758 (mt) cc_final: 0.8553 (mt)
REVERT: C  147 ILE cc_start: 0.8253 (mm) cc_final: 0.7935 (mm)
REVERT: C  176 LEU cc_start: 0.7677 (mt) cc_final: 0.7159 (tt)
REVERT: C  193 ASN cc_start: 0.8939 (m-40) cc_final: 0.8322 (m-40)
REVERT: D  275 GLU cc_start: 0.7101 (pt0) cc_final: 0.6777 (pm20)
REVERT: D  314 LEU cc_start: 0.9223 (mt) cc_final: 0.9015 (mt)
REVERT: D  322 TYR cc_start: 0.7164 (t80) cc_final: 0.5344 (t80)
REVERT: D  335 ASP cc_start: 0.8462 (t0) cc_final: 0.8057 (t0)
REVERT: D  389 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7320 (mptt)
REVERT: D  436 TYR cc_start: 0.7310 (t80) cc_final: 0.7020 (t80)
REVERT: D  551 ASP cc_start: 0.7018 (m-30) cc_final: 0.6301 (t70)
REVERT: E  142 LEU cc_start: 0.8772 (mt) cc_final: 0.8532 (mt)
REVERT: E  147 ILE cc_start: 0.8520 (mm) cc_final: 0.8231 (mm)
REVERT: E  176 LEU cc_start: 0.7649 (mt) cc_final: 0.7430 (tt)
REVERT: F  302 MET cc_start: 0.7358 (mmm) cc_final: 0.7004 (mmt)
REVERT: F  312 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7707 (tp-100)
REVERT: F  389 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7418 (mptt)
REVERT: F  430 TYR cc_start: 0.8360 (m-80) cc_final: 0.7703 (m-80)
REVERT: F  446 CYS cc_start: 0.4461 (t) cc_final: 0.4229 (t)
REVERT: F  463 MET cc_start: 0.6276 (ttm) cc_final: 0.5449 (ttm)
REVERT: F  487 MET cc_start: 0.5585 (tmm) cc_final: 0.5350 (tmm)
REVERT: F  551 ASP cc_start: 0.6814 (m-30) cc_final: 0.5917 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1958
  time to fit residues: 82.4413
Evaluate side-chains
  240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:   20.0000
   chunk 114 optimal weight:    3.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 468 GLN
** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS
F 296 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.160270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.137293 restraints weight = 19827.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.140813 restraints weight = 12837.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.143382 restraints weight = 9311.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.4092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9978  Z= 0.270
  Angle     :  0.666   6.063  13548  Z= 0.356
  Chirality :  0.047   0.206   1647
  Planarity :  0.004   0.041   1716
  Dihedral  :  5.996  32.758   1377
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.23), residues: 1281
  helix:  0.17 (0.28), residues: 345
  sheet: -2.25 (0.42), residues: 117
  loop : -1.76 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP D 423 
 HIS   0.004   0.001   HIS F 250 
 PHE   0.023   0.002   PHE F 491 
 TYR   0.021   0.002   TYR F 293 
 ARG   0.008   0.001   ARG B 277 

*********************** 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
  278 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8945 (mt) cc_final: 0.8740 (mt)
REVERT: A  158 MET cc_start: 0.6503 (tmm) cc_final: 0.6165 (tmm)
REVERT: A  176 LEU cc_start: 0.7662 (mt) cc_final: 0.7329 (tt)
REVERT: A  193 ASN cc_start: 0.9072 (m-40) cc_final: 0.8741 (m-40)
REVERT: B  250 HIS cc_start: 0.6229 (t70) cc_final: 0.5923 (t70)
REVERT: B  275 GLU cc_start: 0.6957 (pt0) cc_final: 0.6729 (pm20)
REVERT: B  314 LEU cc_start: 0.9321 (mt) cc_final: 0.9107 (mt)
REVERT: B  322 TYR cc_start: 0.7577 (t80) cc_final: 0.5986 (t80)
REVERT: B  335 ASP cc_start: 0.8418 (t0) cc_final: 0.8076 (t0)
REVERT: B  385 ASP cc_start: 0.6879 (t70) cc_final: 0.6477 (m-30)
REVERT: B  389 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7518 (mptt)
REVERT: B  487 MET cc_start: 0.5388 (tmm) cc_final: 0.5129 (tmm)
REVERT: C  142 LEU cc_start: 0.8947 (mt) cc_final: 0.8731 (mt)
REVERT: C  147 ILE cc_start: 0.8382 (mm) cc_final: 0.8040 (mm)
REVERT: C  193 ASN cc_start: 0.9013 (m-40) cc_final: 0.8432 (m-40)
REVERT: D  275 GLU cc_start: 0.7170 (pt0) cc_final: 0.6843 (pm20)
REVERT: D  335 ASP cc_start: 0.8265 (t0) cc_final: 0.7856 (t0)
REVERT: D  340 GLU cc_start: 0.7213 (pm20) cc_final: 0.6994 (pm20)
REVERT: D  436 TYR cc_start: 0.7469 (t80) cc_final: 0.7118 (t80)
REVERT: D  487 MET cc_start: 0.5939 (tmm) cc_final: 0.5735 (tmm)
REVERT: D  551 ASP cc_start: 0.7277 (m-30) cc_final: 0.6642 (t70)
REVERT: E  142 LEU cc_start: 0.8897 (mt) cc_final: 0.8659 (mt)
REVERT: E  147 ILE cc_start: 0.8641 (mm) cc_final: 0.8305 (mm)
REVERT: F  305 MET cc_start: 0.2984 (mpp) cc_final: 0.2667 (mtm)
REVERT: F  312 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7960 (tp-100)
REVERT: F  389 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7383 (mptt)
REVERT: F  463 MET cc_start: 0.6653 (ttm) cc_final: 0.6290 (ttm)
REVERT: F  487 MET cc_start: 0.5786 (tmm) cc_final: 0.5468 (tmm)
REVERT: F  551 ASP cc_start: 0.7011 (m-30) cc_final: 0.6246 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.1874
  time to fit residues: 75.3806
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  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 73 optimal weight:    0.6980
   chunk 83 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
B 458 ASN
C 138 HIS
C 209 ASN
E 138 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.156885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.134425 restraints weight = 20246.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.137747 restraints weight = 13461.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140080 restraints weight = 9850.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.4463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9978  Z= 0.309
  Angle     :  0.720   8.267  13548  Z= 0.382
  Chirality :  0.049   0.243   1647
  Planarity :  0.005   0.047   1716
  Dihedral  :  6.306  31.322   1377
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.23), residues: 1281
  helix:  0.46 (0.29), residues: 324
  sheet: -2.25 (0.42), residues: 117
  loop : -1.84 (0.21), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP D 423 
 HIS   0.004   0.001   HIS E 138 
 PHE   0.018   0.003   PHE F 491 
 TYR   0.027   0.003   TYR F 293 
 ARG   0.005   0.001   ARG B 277 

*********************** 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
  259 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 ASN cc_start: 0.9048 (m-40) cc_final: 0.8655 (m-40)
REVERT: B  250 HIS cc_start: 0.6163 (t70) cc_final: 0.5833 (t70)
REVERT: B  335 ASP cc_start: 0.8392 (t0) cc_final: 0.8078 (t0)
REVERT: B  389 LYS cc_start: 0.8569 (mmtt) cc_final: 0.7638 (mptt)
REVERT: B  487 MET cc_start: 0.5729 (tmm) cc_final: 0.5468 (tmm)
REVERT: C  142 LEU cc_start: 0.8906 (mt) cc_final: 0.8698 (mt)
REVERT: C  193 ASN cc_start: 0.9051 (m-40) cc_final: 0.8341 (m-40)
REVERT: D  275 GLU cc_start: 0.7146 (pt0) cc_final: 0.6929 (pm20)
REVERT: D  335 ASP cc_start: 0.8324 (t0) cc_final: 0.7884 (t0)
REVERT: D  340 GLU cc_start: 0.7284 (pm20) cc_final: 0.7080 (pm20)
REVERT: D  463 MET cc_start: 0.6080 (mmm) cc_final: 0.5508 (mmm)
REVERT: D  508 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8189 (ttpt)
REVERT: D  551 ASP cc_start: 0.6973 (m-30) cc_final: 0.6642 (t70)
REVERT: E  142 LEU cc_start: 0.8926 (mt) cc_final: 0.8687 (mt)
REVERT: E  147 ILE cc_start: 0.8623 (mm) cc_final: 0.8264 (mm)
REVERT: F  305 MET cc_start: 0.3128 (mpp) cc_final: 0.2789 (mtm)
REVERT: F  312 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7937 (tp-100)
REVERT: F  389 LYS cc_start: 0.8601 (mmtt) cc_final: 0.7787 (mptt)
REVERT: F  430 TYR cc_start: 0.8837 (m-80) cc_final: 0.8526 (m-80)
REVERT: F  463 MET cc_start: 0.6691 (ttm) cc_final: 0.6331 (ttm)
REVERT: F  487 MET cc_start: 0.6074 (tmm) cc_final: 0.5550 (tmm)
REVERT: F  551 ASP cc_start: 0.7103 (m-30) cc_final: 0.6341 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1755
  time to fit residues: 67.5225
Evaluate side-chains
  215 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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
E 138 HIS
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.156030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.133695 restraints weight = 20256.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.136888 restraints weight = 13501.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.139231 restraints weight = 9927.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9978  Z= 0.313
  Angle     :  0.739   7.055  13548  Z= 0.392
  Chirality :  0.050   0.265   1647
  Planarity :  0.005   0.054   1716
  Dihedral  :  6.404  29.404   1377
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.23), residues: 1281
  helix:  0.45 (0.29), residues: 336
  sheet: -2.11 (0.42), residues: 117
  loop : -1.90 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP D 423 
 HIS   0.003   0.001   HIS E 138 
 PHE   0.019   0.003   PHE F 491 
 TYR   0.028   0.002   TYR F 293 
 ARG   0.006   0.001   ARG B 277 

*********************** 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
  263 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8992 (mt) cc_final: 0.8739 (mt)
REVERT: B  250 HIS cc_start: 0.6227 (t70) cc_final: 0.5882 (t70)
REVERT: B  335 ASP cc_start: 0.8402 (t0) cc_final: 0.8052 (t0)
REVERT: B  463 MET cc_start: 0.7206 (ttm) cc_final: 0.6746 (ttm)
REVERT: B  468 GLN cc_start: 0.8627 (mm110) cc_final: 0.8384 (mm-40)
REVERT: B  487 MET cc_start: 0.5680 (tmm) cc_final: 0.5373 (tmm)
REVERT: B  508 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8085 (ttpt)
REVERT: B  567 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6407 (mm-30)
REVERT: D  322 TYR cc_start: 0.7304 (t80) cc_final: 0.5645 (t80)
REVERT: D  335 ASP cc_start: 0.8343 (t0) cc_final: 0.7864 (t0)
REVERT: D  340 GLU cc_start: 0.7301 (pm20) cc_final: 0.7097 (pm20)
REVERT: D  463 MET cc_start: 0.6290 (mmm) cc_final: 0.5323 (mmm)
REVERT: D  487 MET cc_start: 0.5780 (tmm) cc_final: 0.5541 (tmm)
REVERT: D  508 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8094 (ttpt)
REVERT: D  551 ASP cc_start: 0.7113 (m-30) cc_final: 0.6605 (t70)
REVERT: D  552 MET cc_start: 0.2774 (tpt) cc_final: 0.2567 (tpt)
REVERT: E  147 ILE cc_start: 0.8752 (mm) cc_final: 0.8379 (mm)
REVERT: E  193 ASN cc_start: 0.8801 (m-40) cc_final: 0.8539 (m-40)
REVERT: F  305 MET cc_start: 0.2971 (mpp) cc_final: 0.2542 (mtm)
REVERT: F  322 TYR cc_start: 0.7486 (t80) cc_final: 0.5880 (t80)
REVERT: F  430 TYR cc_start: 0.8810 (m-80) cc_final: 0.8568 (m-80)
REVERT: F  487 MET cc_start: 0.6103 (tmm) cc_final: 0.5528 (tmm)
REVERT: F  551 ASP cc_start: 0.7241 (m-30) cc_final: 0.6414 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.1744
  time to fit residues: 67.7328
Evaluate side-chains
  221 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 96 optimal weight:    0.0970
   chunk 123 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0370
   chunk 91 optimal weight:    0.5980
   chunk 1 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.9460

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

Flipped N/Q/H residues before XYZ refinement:
B 468 GLN
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 193 ASN
C 209 ASN
** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 HIS
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.160847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.137951 restraints weight = 20381.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.141431 restraints weight = 13127.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.143910 restraints weight = 9436.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.4951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9978  Z= 0.199
  Angle     :  0.658   6.840  13548  Z= 0.348
  Chirality :  0.048   0.313   1647
  Planarity :  0.004   0.045   1716
  Dihedral  :  6.001  26.199   1377
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.23), residues: 1281
  helix:  0.58 (0.29), residues: 339
  sheet: -1.88 (0.44), residues: 117
  loop : -1.81 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 423 
 HIS   0.002   0.001   HIS A 163 
 PHE   0.009   0.002   PHE B 448 
 TYR   0.027   0.002   TYR B 430 
 ARG   0.004   0.001   ARG D 334 

*********************** 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
  276 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 ASN cc_start: 0.7572 (t0) cc_final: 0.7316 (t0)
REVERT: B  250 HIS cc_start: 0.6319 (t70) cc_final: 0.6044 (t70)
REVERT: B  314 LEU cc_start: 0.9324 (mt) cc_final: 0.9109 (mt)
REVERT: B  322 TYR cc_start: 0.7471 (t80) cc_final: 0.6053 (t80)
REVERT: B  335 ASP cc_start: 0.8391 (t0) cc_final: 0.7972 (t0)
REVERT: B  385 ASP cc_start: 0.7556 (m-30) cc_final: 0.7093 (m-30)
REVERT: B  389 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7416 (mppt)
REVERT: B  487 MET cc_start: 0.5614 (tmm) cc_final: 0.5358 (tmm)
REVERT: B  508 LYS cc_start: 0.8275 (ttpt) cc_final: 0.8033 (ttpt)
REVERT: B  567 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6221 (mm-30)
REVERT: D  322 TYR cc_start: 0.7259 (t80) cc_final: 0.5570 (t80)
REVERT: D  335 ASP cc_start: 0.8274 (t0) cc_final: 0.7687 (t0)
REVERT: D  340 GLU cc_start: 0.7339 (pm20) cc_final: 0.7088 (pm20)
REVERT: D  436 TYR cc_start: 0.7426 (t80) cc_final: 0.7155 (t80)
REVERT: D  463 MET cc_start: 0.6429 (mmm) cc_final: 0.5860 (mmm)
REVERT: D  487 MET cc_start: 0.5977 (tmm) cc_final: 0.5738 (tmm)
REVERT: D  508 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8112 (tmmt)
REVERT: D  510 TYR cc_start: 0.7205 (t80) cc_final: 0.6645 (t80)
REVERT: D  551 ASP cc_start: 0.7187 (m-30) cc_final: 0.6313 (t70)
REVERT: E  142 LEU cc_start: 0.8911 (mt) cc_final: 0.8671 (mt)
REVERT: E  193 ASN cc_start: 0.8813 (m-40) cc_final: 0.8543 (m-40)
REVERT: F  305 MET cc_start: 0.3004 (mpp) cc_final: 0.2518 (mtm)
REVERT: F  430 TYR cc_start: 0.8646 (m-80) cc_final: 0.8293 (m-80)
REVERT: F  487 MET cc_start: 0.6058 (tmm) cc_final: 0.5450 (tmm)
REVERT: F  547 ARG cc_start: 0.5014 (tpp-160) cc_final: 0.4765 (mmt-90)
REVERT: F  551 ASP cc_start: 0.7080 (m-30) cc_final: 0.5939 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.1945
  time to fit residues: 76.6603
Evaluate side-chains
  233 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 4 optimal weight:    5.9990
   chunk 101 optimal weight:    0.4980
   chunk 22 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 120 optimal weight:   10.0000
   chunk 37 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 574 ASN
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 ASN
C 209 ASN
D 574 ASN
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 574 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.164934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.143291 restraints weight = 20038.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.146556 restraints weight = 13232.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.148882 restraints weight = 9649.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9978  Z= 0.165
  Angle     :  0.640   9.493  13548  Z= 0.334
  Chirality :  0.048   0.302   1647
  Planarity :  0.004   0.043   1716
  Dihedral  :  5.576  22.993   1377
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.23), residues: 1281
  helix:  0.91 (0.29), residues: 321
  sheet: -1.71 (0.45), residues: 117
  loop : -1.71 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 423 
 HIS   0.003   0.001   HIS C 138 
 PHE   0.021   0.002   PHE D 491 
 TYR   0.027   0.001   TYR F 322 
 ARG   0.008   0.001   ARG F 277 

*********************** 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
  280 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  322 TYR cc_start: 0.7133 (t80) cc_final: 0.5970 (t80)
REVERT: B  335 ASP cc_start: 0.8281 (t0) cc_final: 0.7971 (t0)
REVERT: B  385 ASP cc_start: 0.7197 (m-30) cc_final: 0.6926 (m-30)
REVERT: B  389 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7627 (mptt)
REVERT: B  463 MET cc_start: 0.7362 (ttm) cc_final: 0.7158 (ttm)
REVERT: B  508 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7908 (ttpt)
REVERT: B  567 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5960 (mm-30)
REVERT: C  195 VAL cc_start: 0.8737 (t) cc_final: 0.8522 (t)
REVERT: D  322 TYR cc_start: 0.7101 (t80) cc_final: 0.5520 (t80)
REVERT: D  335 ASP cc_start: 0.8294 (t0) cc_final: 0.7737 (t0)
REVERT: D  340 GLU cc_start: 0.7302 (pm20) cc_final: 0.7068 (pm20)
REVERT: D  371 ILE cc_start: 0.8518 (mm) cc_final: 0.8131 (mp)
REVERT: D  463 MET cc_start: 0.6485 (mmm) cc_final: 0.5872 (mmm)
REVERT: D  508 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7949 (ttpt)
REVERT: D  532 CYS cc_start: 0.5063 (p) cc_final: 0.4634 (t)
REVERT: D  551 ASP cc_start: 0.7014 (m-30) cc_final: 0.6233 (t70)
REVERT: E  142 LEU cc_start: 0.8774 (mt) cc_final: 0.8520 (mt)
REVERT: E  193 ASN cc_start: 0.8712 (m-40) cc_final: 0.8386 (m-40)
REVERT: F  389 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8493 (mmtt)
REVERT: F  463 MET cc_start: 0.6763 (ttm) cc_final: 0.6068 (ttm)
REVERT: F  468 GLN cc_start: 0.8508 (mm110) cc_final: 0.8292 (mm110)
REVERT: F  487 MET cc_start: 0.5916 (tmm) cc_final: 0.5452 (tmm)
REVERT: F  547 ARG cc_start: 0.5134 (tpp-160) cc_final: 0.4907 (mmt180)
REVERT: F  551 ASP cc_start: 0.6948 (m-30) cc_final: 0.5952 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.2009
  time to fit residues: 80.0298
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  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 107 optimal weight:    9.9990
   chunk 97 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    4.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 209 ASN
B 458 ASN
B 468 GLN
B 574 ASN
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
D 409 HIS
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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.155761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.132910 restraints weight = 21522.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.136247 restraints weight = 14293.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138608 restraints weight = 10491.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9978  Z= 0.331
  Angle     :  0.788   8.808  13548  Z= 0.412
  Chirality :  0.051   0.320   1647
  Planarity :  0.005   0.058   1716
  Dihedral  :  6.322  29.260   1377
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.72 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.23), residues: 1281
  helix:  0.49 (0.29), residues: 339
  sheet: -1.86 (0.43), residues: 117
  loop : -1.89 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP D 423 
 HIS   0.004   0.001   HIS A 138 
 PHE   0.027   0.003   PHE D 491 
 TYR   0.031   0.003   TYR F 293 
 ARG   0.006   0.001   ARG F 277 

*********************** 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
  272 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 ASN cc_start: 0.9035 (m110) cc_final: 0.8756 (m-40)
REVERT: B  251 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7009 (mp10)
REVERT: B  335 ASP cc_start: 0.8359 (t0) cc_final: 0.7927 (t0)
REVERT: B  340 GLU cc_start: 0.7308 (pm20) cc_final: 0.7043 (pm20)
REVERT: B  389 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7743 (mptt)
REVERT: B  508 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7961 (ttpt)
REVERT: C  195 VAL cc_start: 0.8786 (t) cc_final: 0.8455 (t)
REVERT: D  322 TYR cc_start: 0.7431 (t80) cc_final: 0.5633 (t80)
REVERT: D  335 ASP cc_start: 0.8283 (t0) cc_final: 0.7756 (t0)
REVERT: D  340 GLU cc_start: 0.7190 (pm20) cc_final: 0.6895 (pm20)
REVERT: D  429 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7428 (tpt170)
REVERT: D  463 MET cc_start: 0.6579 (mmm) cc_final: 0.5869 (mmm)
REVERT: D  487 MET cc_start: 0.6084 (tmm) cc_final: 0.4413 (mtm)
REVERT: D  510 TYR cc_start: 0.7260 (t80) cc_final: 0.6637 (t80)
REVERT: D  551 ASP cc_start: 0.7275 (m-30) cc_final: 0.6298 (t70)
REVERT: D  567 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6244 (mm-30)
REVERT: E  142 LEU cc_start: 0.9003 (mt) cc_final: 0.8788 (mt)
REVERT: F  308 GLU cc_start: 0.5785 (mp0) cc_final: 0.5465 (mp0)
REVERT: F  430 TYR cc_start: 0.8923 (m-80) cc_final: 0.8626 (m-80)
REVERT: F  487 MET cc_start: 0.6095 (tmm) cc_final: 0.5601 (tmm)
REVERT: F  551 ASP cc_start: 0.7081 (m-30) cc_final: 0.5962 (t70)
REVERT: F  570 ASP cc_start: 0.7733 (m-30) cc_final: 0.7514 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 272
  average time/residue: 0.1987
  time to fit residues: 77.4770
Evaluate side-chains
  217 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 94 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 81 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 106 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 209 ASN
B 257 GLN
** C 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 209 ASN
** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 409 HIS
** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.157953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.134902 restraints weight = 21104.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.138298 restraints weight = 13975.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.140697 restraints weight = 10215.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9978  Z= 0.257
  Angle     :  0.749   9.430  13548  Z= 0.393
  Chirality :  0.050   0.327   1647
  Planarity :  0.005   0.042   1716
  Dihedral  :  6.185  27.658   1377
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.23), residues: 1281
  helix:  0.21 (0.28), residues: 354
  sheet: -1.80 (0.43), residues: 117
  loop : -1.93 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP D 423 
 HIS   0.004   0.001   HIS E 138 
 PHE   0.010   0.002   PHE F 526 
 TYR   0.023   0.002   TYR B 293 
 ARG   0.007   0.001   ARG F 277 

********************** 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
  262 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  322 TYR cc_start: 0.7571 (t80) cc_final: 0.5930 (t80)
REVERT: B  335 ASP cc_start: 0.8339 (t0) cc_final: 0.7898 (t0)
REVERT: B  340 GLU cc_start: 0.7375 (pm20) cc_final: 0.7134 (pm20)
REVERT: B  389 LYS cc_start: 0.8587 (mmtt) cc_final: 0.7678 (mptt)
REVERT: B  508 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7943 (ttpt)
REVERT: D  335 ASP cc_start: 0.8256 (t0) cc_final: 0.7632 (t0)
REVERT: D  340 GLU cc_start: 0.7269 (pm20) cc_final: 0.6972 (pm20)
REVERT: D  371 ILE cc_start: 0.8821 (mm) cc_final: 0.8457 (mp)
REVERT: D  463 MET cc_start: 0.6433 (mmm) cc_final: 0.5870 (mmm)
REVERT: D  510 TYR cc_start: 0.7402 (t80) cc_final: 0.6855 (t80)
REVERT: D  551 ASP cc_start: 0.7100 (m-30) cc_final: 0.6277 (t70)
REVERT: E  197 GLU cc_start: 0.8254 (mp0) cc_final: 0.8035 (mp0)
REVERT: F  308 GLU cc_start: 0.5806 (mp0) cc_final: 0.5551 (mp0)
REVERT: F  321 TYR cc_start: 0.8013 (t80) cc_final: 0.7760 (t80)
REVERT: F  430 TYR cc_start: 0.8827 (m-80) cc_final: 0.8530 (m-80)
REVERT: F  487 MET cc_start: 0.6022 (tmm) cc_final: 0.5417 (tmm)
REVERT: F  551 ASP cc_start: 0.7172 (m-30) cc_final: 0.5938 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1994
  time to fit residues: 76.9161
Evaluate side-chains
  224 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0970
   chunk 101 optimal weight:    0.3980
   chunk 72 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    1.8984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.160599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.137292 restraints weight = 20894.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140729 restraints weight = 13912.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.143192 restraints weight = 10190.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9978  Z= 0.201
  Angle     :  0.692   8.521  13548  Z= 0.361
  Chirality :  0.049   0.324   1647
  Planarity :  0.004   0.044   1716
  Dihedral  :  5.830  25.016   1377
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.23), residues: 1281
  helix:  0.25 (0.28), residues: 348
  sheet: -1.57 (0.45), residues: 117
  loop : -1.74 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 423 
 HIS   0.003   0.001   HIS A 138 
 PHE   0.010   0.002   PHE F 526 
 TYR   0.024   0.002   TYR F 322 
 ARG   0.007   0.001   ARG F 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3018.01 seconds
wall clock time: 54 minutes 29.82 seconds (3269.82 seconds total)