Starting phenix.real_space_refine
on Fri Feb 14 01:46:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xye_10649/02_2025/6xye_10649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xye_10649/02_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_10649/02_2025/6xye_10649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xye_10649/02_2025/6xye_10649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xye_10649/02_2025/6xye_10649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xye_10649/02_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-5592/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: 5.02, per 1000 atoms: 0.51
  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=5, 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

  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: 2.66
  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: 1.25
  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: 3.01

  Time building geometry restraints manager: 2.89 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: 5645
       14.85 -    29.69: 414
       29.69 -    44.53: 37
       44.53 -    59.38: 3
       59.38 -    74.22: 3
  Dihedral angle restraints: 6102
    sinusoidal: 2364
      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 6099 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:
        2.02 -     2.60: 114
        2.60 -     3.17: 8547
        3.17 -     3.75: 14635
        3.75 -     4.32: 19499
        4.32 -     4.90: 31135
  Nonbonded interactions: 73930
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D 470 "
            pdb=" SG  CYS D 478 "
     model   vdw
     2.020 3.760
  nonbonded pdb=" SG  CYS F 470 "
            pdb=" SG  CYS F 478 "
     model   vdw
     2.021 3.760
  nonbonded pdb=" SG  CYS D 502 "
            pdb=" SG  CYS D 507 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS F 502 "
            pdb=" SG  CYS F 507 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS F 509 "
            pdb=" SG  CYS F 532 "
     model   vdw
     2.036 3.760
  ... (remaining 73925 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:             0.180
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.630
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.310
-------------------------------------------------------------------------------
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= 0.663
  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 : 2.020

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  : 1.020 
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: 0.2392
  time to fit residues: 122.6457
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  : 1.112 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 114 optimal weight:    7.9990
   overall best weight:    0.7398

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

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

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.165239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.142544 restraints weight = 19425.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.146173 restraints weight = 12817.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.148798 restraints weight = 9320.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9978  Z= 0.179
  Angle     :  0.661   7.541  13548  Z= 0.349
  Chirality :  0.047   0.340   1647
  Planarity :  0.004   0.035   1716
  Dihedral  :  6.273  35.565   1377
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.13 (0.22), residues: 1281
  helix: -0.55 (0.26), residues: 363
  sheet: -2.58 (0.44), residues: 105
  loop : -1.72 (0.21), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 423 
 HIS   0.003   0.001   HIS D 250 
 PHE   0.010   0.002   PHE D 329 
 TYR   0.015   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
  315 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 315
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8856 (mt) cc_final: 0.8588 (mt)
REVERT: A  147 ILE cc_start: 0.8460 (mm) cc_final: 0.8223 (mm)
REVERT: A  193 ASN cc_start: 0.8858 (m-40) cc_final: 0.8381 (m-40)
REVERT: B  314 LEU cc_start: 0.9218 (mt) cc_final: 0.9008 (mt)
REVERT: B  322 TYR cc_start: 0.7152 (t80) cc_final: 0.6199 (t80)
REVERT: B  385 ASP cc_start: 0.6730 (t70) cc_final: 0.6363 (m-30)
REVERT: B  389 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7315 (mptt)
REVERT: B  408 VAL cc_start: 0.8467 (t) cc_final: 0.8251 (t)
REVERT: B  411 LEU cc_start: 0.8317 (mt) cc_final: 0.8097 (mp)
REVERT: B  412 GLU cc_start: 0.8269 (tp30) cc_final: 0.7596 (tp30)
REVERT: B  551 ASP cc_start: 0.7313 (m-30) cc_final: 0.6755 (t70)
REVERT: C  142 LEU cc_start: 0.8845 (mt) cc_final: 0.8611 (mt)
REVERT: C  147 ILE cc_start: 0.8313 (mm) cc_final: 0.8028 (mm)
REVERT: C  176 LEU cc_start: 0.7727 (mt) cc_final: 0.7228 (tt)
REVERT: C  193 ASN cc_start: 0.8872 (m-40) cc_final: 0.8339 (m-40)
REVERT: D  275 GLU cc_start: 0.7154 (pt0) cc_final: 0.6717 (pm20)
REVERT: D  389 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7438 (mptt)
REVERT: D  436 TYR cc_start: 0.7411 (t80) cc_final: 0.7029 (t80)
REVERT: D  551 ASP cc_start: 0.7148 (m-30) cc_final: 0.6656 (t70)
REVERT: F  275 GLU cc_start: 0.7029 (pt0) cc_final: 0.6817 (pm20)
REVERT: F  302 MET cc_start: 0.7355 (mmm) cc_final: 0.7044 (mmt)
REVERT: F  314 LEU cc_start: 0.9201 (mt) cc_final: 0.8979 (mt)
REVERT: F  322 TYR cc_start: 0.7428 (t80) cc_final: 0.7187 (t80)
REVERT: F  385 ASP cc_start: 0.8019 (m-30) cc_final: 0.7642 (m-30)
REVERT: F  389 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7622 (mptt)
REVERT: F  430 TYR cc_start: 0.8237 (m-80) cc_final: 0.7543 (m-80)
REVERT: F  508 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8024 (ttpp)
REVERT: F  510 TYR cc_start: 0.6936 (t80) cc_final: 0.6463 (t80)
REVERT: F  551 ASP cc_start: 0.7499 (m-30) cc_final: 0.6701 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 315
  average time/residue: 0.2089
  time to fit residues: 91.9371
Evaluate side-chains
  247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 35 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 105 optimal weight:    0.0050
   chunk 91 optimal weight:    3.9990
   chunk 114 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 7 optimal weight:   20.0000
   chunk 10 optimal weight:    0.0270
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.4056

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

Flipped N/Q/H residues before XYZ refinement:
B 296 ASN
B 312 GLN
B 497 ASN
B 518 GLN
C 138 HIS
D 312 GLN
D 383 HIS
E 138 HIS
F 296 ASN
F 312 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.164451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.142437 restraints weight = 19511.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.145801 restraints weight = 13001.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.148312 restraints weight = 9551.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9978  Z= 0.170
  Angle     :  0.608   6.528  13548  Z= 0.322
  Chirality :  0.046   0.219   1647
  Planarity :  0.004   0.038   1716
  Dihedral  :  5.850  27.502   1377
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.23), residues: 1281
  helix: -0.08 (0.27), residues: 360
  sheet: -2.15 (0.52), residues: 87
  loop : -1.71 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 423 
 HIS   0.003   0.001   HIS D 250 
 PHE   0.008   0.002   PHE D 329 
 TYR   0.014   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  : 1.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8844 (mt) cc_final: 0.8626 (mt)
REVERT: A  150 THR cc_start: 0.7605 (p) cc_final: 0.7394 (t)
REVERT: A  158 MET cc_start: 0.6859 (tmm) cc_final: 0.6581 (tmm)
REVERT: A  176 LEU cc_start: 0.7665 (mt) cc_final: 0.7351 (tt)
REVERT: A  193 ASN cc_start: 0.8893 (m-40) cc_final: 0.8421 (m-40)
REVERT: B  250 HIS cc_start: 0.6257 (t70) cc_final: 0.5940 (t70)
REVERT: B  314 LEU cc_start: 0.9100 (mt) cc_final: 0.8897 (mt)
REVERT: B  322 TYR cc_start: 0.6998 (t80) cc_final: 0.6433 (t80)
REVERT: B  335 ASP cc_start: 0.8357 (t0) cc_final: 0.8135 (t0)
REVERT: B  385 ASP cc_start: 0.6861 (t70) cc_final: 0.6371 (m-30)
REVERT: B  389 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7232 (mptt)
REVERT: B  487 MET cc_start: 0.5770 (tmm) cc_final: 0.5517 (tmm)
REVERT: B  547 ARG cc_start: 0.4925 (ttm110) cc_final: 0.4498 (ttm170)
REVERT: C  147 ILE cc_start: 0.8255 (mm) cc_final: 0.7934 (mm)
REVERT: C  176 LEU cc_start: 0.7653 (mt) cc_final: 0.7224 (tt)
REVERT: C  193 ASN cc_start: 0.8920 (m-40) cc_final: 0.8351 (m-40)
REVERT: D  275 GLU cc_start: 0.7103 (pt0) cc_final: 0.6803 (pm20)
REVERT: D  314 LEU cc_start: 0.9215 (mt) cc_final: 0.9010 (mt)
REVERT: D  335 ASP cc_start: 0.8495 (t0) cc_final: 0.8135 (t0)
REVERT: D  389 LYS cc_start: 0.8434 (mmtt) cc_final: 0.7388 (mptt)
REVERT: D  436 TYR cc_start: 0.7373 (t80) cc_final: 0.7018 (t80)
REVERT: D  508 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8127 (ttpt)
REVERT: D  551 ASP cc_start: 0.6947 (m-30) cc_final: 0.6565 (t70)
REVERT: E  142 LEU cc_start: 0.8742 (mt) cc_final: 0.8508 (mt)
REVERT: E  147 ILE cc_start: 0.8488 (mm) cc_final: 0.8217 (mm)
REVERT: E  150 THR cc_start: 0.7603 (p) cc_final: 0.7254 (m)
REVERT: F  302 MET cc_start: 0.7328 (mmm) cc_final: 0.6995 (mmt)
REVERT: F  389 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7472 (mptt)
REVERT: F  430 TYR cc_start: 0.8441 (m-80) cc_final: 0.7864 (m-80)
REVERT: F  463 MET cc_start: 0.6546 (ttm) cc_final: 0.5175 (ttm)
REVERT: F  468 GLN cc_start: 0.8410 (mm110) cc_final: 0.6754 (mm-40)
REVERT: F  487 MET cc_start: 0.5711 (tmm) cc_final: 0.5507 (tmm)
REVERT: F  508 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7612 (ttpp)
REVERT: F  551 ASP cc_start: 0.7327 (m-30) cc_final: 0.6141 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.2112
  time to fit residues: 88.7587
Evaluate side-chains
  229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 100 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0870
   chunk 114 optimal weight:    9.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    3.8166

-------------------------------------------------------------------------------
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 468 GLN
C 138 HIS
D 295 ASN
E 138 HIS
F 295 ASN
F 296 ASN
F 312 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.157871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135231 restraints weight = 20005.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.138541 restraints weight = 13422.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.140897 restraints weight = 9906.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9978  Z= 0.290
  Angle     :  0.700   6.861  13548  Z= 0.369
  Chirality :  0.048   0.199   1647
  Planarity :  0.005   0.041   1716
  Dihedral  :  6.030  26.947   1377
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.23), residues: 1281
  helix:  0.08 (0.28), residues: 345
  sheet: -2.49 (0.41), residues: 117
  loop : -1.70 (0.22), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP B 423 
 HIS   0.003   0.001   HIS D 250 
 PHE   0.027   0.003   PHE D 491 
 TYR   0.023   0.002   TYR F 293 
 ARG   0.004   0.001   ARG B 480 

*********************** 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
  280 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.9020 (mt) cc_final: 0.8789 (mt)
REVERT: A  147 ILE cc_start: 0.8659 (mm) cc_final: 0.8256 (mm)
REVERT: A  158 MET cc_start: 0.6804 (tmm) cc_final: 0.6346 (tmm)
REVERT: A  176 LEU cc_start: 0.7673 (mt) cc_final: 0.7328 (tt)
REVERT: A  193 ASN cc_start: 0.9057 (m-40) cc_final: 0.8714 (m-40)
REVERT: B  250 HIS cc_start: 0.6280 (t70) cc_final: 0.5917 (t70)
REVERT: B  335 ASP cc_start: 0.8363 (t0) cc_final: 0.8048 (t0)
REVERT: B  389 LYS cc_start: 0.8565 (mmtt) cc_final: 0.7602 (mptt)
REVERT: B  463 MET cc_start: 0.7067 (ttm) cc_final: 0.6600 (ttm)
REVERT: B  487 MET cc_start: 0.5423 (tmm) cc_final: 0.5156 (tmm)
REVERT: C  142 LEU cc_start: 0.9004 (mt) cc_final: 0.8753 (mt)
REVERT: C  147 ILE cc_start: 0.8376 (mm) cc_final: 0.8171 (mm)
REVERT: C  176 LEU cc_start: 0.7524 (mt) cc_final: 0.7119 (tt)
REVERT: C  193 ASN cc_start: 0.9112 (m-40) cc_final: 0.8475 (m-40)
REVERT: D  275 GLU cc_start: 0.7200 (pt0) cc_final: 0.6879 (pm20)
REVERT: D  322 TYR cc_start: 0.7532 (t80) cc_final: 0.7285 (t80)
REVERT: D  335 ASP cc_start: 0.8277 (t0) cc_final: 0.7824 (t0)
REVERT: D  436 TYR cc_start: 0.7392 (t80) cc_final: 0.7077 (t80)
REVERT: D  487 MET cc_start: 0.5886 (tmm) cc_final: 0.5650 (tmm)
REVERT: D  508 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8104 (ttpt)
REVERT: D  543 GLN cc_start: 0.7331 (tt0) cc_final: 0.6868 (tp40)
REVERT: D  551 ASP cc_start: 0.7188 (m-30) cc_final: 0.6698 (t70)
REVERT: E  142 LEU cc_start: 0.8932 (mt) cc_final: 0.8685 (mt)
REVERT: E  147 ILE cc_start: 0.8626 (mm) cc_final: 0.8284 (mm)
REVERT: F  389 LYS cc_start: 0.8490 (mmtt) cc_final: 0.7513 (mptt)
REVERT: F  430 TYR cc_start: 0.8763 (m-80) cc_final: 0.8436 (m-80)
REVERT: F  463 MET cc_start: 0.6564 (ttm) cc_final: 0.5936 (ttm)
REVERT: F  468 GLN cc_start: 0.8545 (mm110) cc_final: 0.8267 (mm110)
REVERT: F  487 MET cc_start: 0.5722 (tmm) cc_final: 0.5357 (tmm)
REVERT: F  551 ASP cc_start: 0.7504 (m-30) cc_final: 0.6221 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.2022
  time to fit residues: 80.7583
Evaluate side-chains
  222 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 83 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 109 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    2.2384

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.160252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.137841 restraints weight = 20105.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.141190 restraints weight = 13387.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.143634 restraints weight = 9845.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9978  Z= 0.206
  Angle     :  0.639   9.018  13548  Z= 0.335
  Chirality :  0.047   0.249   1647
  Planarity :  0.004   0.042   1716
  Dihedral  :  5.760  26.513   1377
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  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 : 0.00 %

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: -1.73 (0.23), residues: 1281
  helix:  0.53 (0.29), residues: 324
  sheet: -2.18 (0.42), residues: 117
  loop : -1.77 (0.21), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 423 
 HIS   0.002   0.001   HIS A 163 
 PHE   0.014   0.002   PHE F 491 
 TYR   0.016   0.002   TYR F 293 
 ARG   0.009   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
  274 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8928 (mt) cc_final: 0.8682 (mt)
REVERT: A  147 ILE cc_start: 0.8550 (mm) cc_final: 0.8144 (mm)
REVERT: A  150 THR cc_start: 0.7577 (p) cc_final: 0.7344 (m)
REVERT: A  176 LEU cc_start: 0.7416 (mt) cc_final: 0.7137 (tt)
REVERT: B  250 HIS cc_start: 0.6356 (t70) cc_final: 0.6103 (t70)
REVERT: B  314 LEU cc_start: 0.9202 (mt) cc_final: 0.8956 (mt)
REVERT: B  322 TYR cc_start: 0.7473 (t80) cc_final: 0.6417 (t80)
REVERT: B  335 ASP cc_start: 0.8366 (t0) cc_final: 0.8018 (t0)
REVERT: B  463 MET cc_start: 0.7137 (ttm) cc_final: 0.6730 (ttm)
REVERT: B  487 MET cc_start: 0.5493 (tmm) cc_final: 0.5167 (tmm)
REVERT: C  142 LEU cc_start: 0.8907 (mt) cc_final: 0.8645 (mt)
REVERT: C  176 LEU cc_start: 0.7421 (mt) cc_final: 0.7066 (tt)
REVERT: C  193 ASN cc_start: 0.9097 (m-40) cc_final: 0.8475 (m-40)
REVERT: D  275 GLU cc_start: 0.7196 (pt0) cc_final: 0.6922 (pm20)
REVERT: D  322 TYR cc_start: 0.7292 (t80) cc_final: 0.5510 (t80)
REVERT: D  335 ASP cc_start: 0.8262 (t0) cc_final: 0.7767 (t0)
REVERT: D  436 TYR cc_start: 0.7308 (t80) cc_final: 0.6996 (t80)
REVERT: D  487 MET cc_start: 0.5862 (tmm) cc_final: 0.5570 (tmm)
REVERT: D  508 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8064 (ttpt)
REVERT: D  543 GLN cc_start: 0.7364 (tt0) cc_final: 0.6859 (tp40)
REVERT: D  551 ASP cc_start: 0.7143 (m-30) cc_final: 0.6583 (t70)
REVERT: E  142 LEU cc_start: 0.8845 (mt) cc_final: 0.8609 (mt)
REVERT: E  147 ILE cc_start: 0.8625 (mm) cc_final: 0.8279 (mm)
REVERT: F  389 LYS cc_start: 0.8518 (mmtt) cc_final: 0.7665 (mptt)
REVERT: F  430 TYR cc_start: 0.8664 (m-80) cc_final: 0.8335 (m-80)
REVERT: F  463 MET cc_start: 0.6334 (ttm) cc_final: 0.5633 (ttm)
REVERT: F  468 GLN cc_start: 0.8387 (mm110) cc_final: 0.8137 (mm110)
REVERT: F  487 MET cc_start: 0.5685 (tmm) cc_final: 0.5367 (tmm)
REVERT: F  547 ARG cc_start: 0.4838 (ttm110) cc_final: 0.4179 (tpp-160)
REVERT: F  551 ASP cc_start: 0.7329 (m-30) cc_final: 0.5769 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.1979
  time to fit residues: 77.3037
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  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0870
   chunk 69 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    1.9762

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.161115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.138660 restraints weight = 19929.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.142116 restraints weight = 13224.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.144549 restraints weight = 9667.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.4647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9978  Z= 0.189
  Angle     :  0.621   7.131  13548  Z= 0.326
  Chirality :  0.047   0.250   1647
  Planarity :  0.004   0.046   1716
  Dihedral  :  5.580  24.308   1377
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  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: -1.47 (0.23), residues: 1281
  helix:  0.87 (0.29), residues: 324
  sheet: -2.10 (0.43), residues: 117
  loop : -1.65 (0.22), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 423 
 HIS   0.002   0.000   HIS F 250 
 PHE   0.008   0.001   PHE D 526 
 TYR   0.021   0.001   TYR F 322 
 ARG   0.009   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
  276 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 LEU cc_start: 0.8917 (mt) cc_final: 0.8703 (mt)
REVERT: A  147 ILE cc_start: 0.8553 (mm) cc_final: 0.8145 (mm)
REVERT: A  193 ASN cc_start: 0.8749 (m-40) cc_final: 0.8478 (m-40)
REVERT: A  195 VAL cc_start: 0.8905 (t) cc_final: 0.8705 (t)
REVERT: B  314 LEU cc_start: 0.9104 (mt) cc_final: 0.8903 (mt)
REVERT: B  322 TYR cc_start: 0.7512 (t80) cc_final: 0.6319 (t80)
REVERT: B  335 ASP cc_start: 0.8326 (t0) cc_final: 0.7952 (t0)
REVERT: B  385 ASP cc_start: 0.7480 (m-30) cc_final: 0.7153 (m-30)
REVERT: B  463 MET cc_start: 0.7271 (ttm) cc_final: 0.6898 (ttm)
REVERT: B  487 MET cc_start: 0.5501 (tmm) cc_final: 0.5235 (tmm)
REVERT: B  508 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7967 (ttpt)
REVERT: C  147 ILE cc_start: 0.8508 (mm) cc_final: 0.8263 (mm)
REVERT: C  193 ASN cc_start: 0.9075 (m-40) cc_final: 0.8499 (m-40)
REVERT: D  275 GLU cc_start: 0.7192 (pt0) cc_final: 0.6909 (pm20)
REVERT: D  322 TYR cc_start: 0.7360 (t80) cc_final: 0.5688 (t80)
REVERT: D  335 ASP cc_start: 0.8209 (t0) cc_final: 0.7597 (t0)
REVERT: D  487 MET cc_start: 0.5832 (tmm) cc_final: 0.5584 (tmm)
REVERT: D  508 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8029 (ttpt)
REVERT: D  551 ASP cc_start: 0.7216 (m-30) cc_final: 0.6586 (t70)
REVERT: E  147 ILE cc_start: 0.8554 (mm) cc_final: 0.8165 (mm)
REVERT: F  321 TYR cc_start: 0.7877 (t80) cc_final: 0.7667 (t80)
REVERT: F  389 LYS cc_start: 0.8530 (mmtt) cc_final: 0.7663 (mptt)
REVERT: F  430 TYR cc_start: 0.8686 (m-80) cc_final: 0.8361 (m-80)
REVERT: F  463 MET cc_start: 0.6396 (ttm) cc_final: 0.5894 (ttm)
REVERT: F  487 MET cc_start: 0.5719 (tmm) cc_final: 0.5342 (tmm)
REVERT: F  551 ASP cc_start: 0.7431 (m-30) cc_final: 0.6162 (t70)
REVERT: F  570 ASP cc_start: 0.7509 (m-30) cc_final: 0.7305 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.1951
  time to fit residues: 76.7891
Evaluate side-chains
  226 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 96 optimal weight:    8.9990
   chunk 123 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 91 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7184

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.163815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.141634 restraints weight = 19982.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.145145 restraints weight = 13072.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.147703 restraints weight = 9504.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.4870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9978  Z= 0.159
  Angle     :  0.605   6.975  13548  Z= 0.318
  Chirality :  0.046   0.277   1647
  Planarity :  0.004   0.043   1716
  Dihedral  :  5.317  21.642   1377
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.36 (0.23), residues: 1281
  helix:  0.95 (0.29), residues: 324
  sheet: -1.94 (0.43), residues: 117
  loop : -1.58 (0.21), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 423 
 HIS   0.002   0.000   HIS A 163 
 PHE   0.008   0.001   PHE D 526 
 TYR   0.015   0.001   TYR D 436 
 ARG   0.006   0.001   ARG B 277 

*********************** 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
  280 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8516 (mm) cc_final: 0.8112 (mm)
REVERT: B  308 GLU cc_start: 0.5076 (mp0) cc_final: 0.4866 (mp0)
REVERT: B  322 TYR cc_start: 0.7417 (t80) cc_final: 0.6243 (t80)
REVERT: B  335 ASP cc_start: 0.8301 (t0) cc_final: 0.8020 (t0)
REVERT: B  463 MET cc_start: 0.7294 (ttm) cc_final: 0.7036 (ttm)
REVERT: B  487 MET cc_start: 0.5257 (tmm) cc_final: 0.5005 (tmm)
REVERT: C  193 ASN cc_start: 0.9043 (m-40) cc_final: 0.8493 (m-40)
REVERT: D  250 HIS cc_start: 0.6696 (t70) cc_final: 0.6473 (t70)
REVERT: D  275 GLU cc_start: 0.7189 (pt0) cc_final: 0.6921 (pm20)
REVERT: D  322 TYR cc_start: 0.7238 (t80) cc_final: 0.5661 (t80)
REVERT: D  335 ASP cc_start: 0.8207 (t0) cc_final: 0.7603 (t0)
REVERT: D  389 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8251 (mmtt)
REVERT: D  436 TYR cc_start: 0.7307 (t80) cc_final: 0.7082 (t80)
REVERT: D  487 MET cc_start: 0.5778 (tmm) cc_final: 0.5562 (tmm)
REVERT: D  508 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7977 (ttpt)
REVERT: D  551 ASP cc_start: 0.6982 (m-30) cc_final: 0.6192 (t70)
REVERT: E  142 LEU cc_start: 0.8792 (mt) cc_final: 0.8544 (mt)
REVERT: E  147 ILE cc_start: 0.8561 (mm) cc_final: 0.8350 (mm)
REVERT: F  385 ASP cc_start: 0.7607 (m-30) cc_final: 0.7183 (m-30)
REVERT: F  389 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7676 (mptt)
REVERT: F  430 TYR cc_start: 0.8620 (m-80) cc_final: 0.8247 (m-80)
REVERT: F  463 MET cc_start: 0.6539 (ttm) cc_final: 0.6129 (ttm)
REVERT: F  487 MET cc_start: 0.5578 (tmm) cc_final: 0.5250 (tmm)
REVERT: F  551 ASP cc_start: 0.7297 (m-30) cc_final: 0.6131 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1991
  time to fit residues: 79.3050
Evaluate side-chains
  227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 22 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 76 optimal weight:    0.5980
   overall best weight:    1.9986

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.161354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.139562 restraints weight = 19978.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.142935 restraints weight = 13223.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.145251 restraints weight = 9649.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.4959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9978  Z= 0.191
  Angle     :  0.628   9.781  13548  Z= 0.327
  Chirality :  0.047   0.272   1647
  Planarity :  0.004   0.043   1716
  Dihedral  :  5.350  21.159   1377
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.23), residues: 1281
  helix:  0.98 (0.29), residues: 324
  sheet: -1.78 (0.44), residues: 117
  loop : -1.59 (0.21), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 423 
 HIS   0.002   0.000   HIS A 163 
 PHE   0.010   0.002   PHE D 526 
 TYR   0.020   0.002   TYR F 322 
 ARG   0.006   0.001   ARG B 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
  277 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8564 (mm) cc_final: 0.8317 (mm)
REVERT: B  308 GLU cc_start: 0.5096 (mp0) cc_final: 0.4885 (mp0)
REVERT: B  335 ASP cc_start: 0.8327 (t0) cc_final: 0.8067 (t0)
REVERT: B  385 ASP cc_start: 0.7273 (m-30) cc_final: 0.7033 (m-30)
REVERT: B  463 MET cc_start: 0.7316 (ttm) cc_final: 0.7063 (ttm)
REVERT: C  193 ASN cc_start: 0.9026 (m-40) cc_final: 0.8421 (m-40)
REVERT: D  250 HIS cc_start: 0.6645 (t70) cc_final: 0.6435 (t70)
REVERT: D  335 ASP cc_start: 0.8252 (t0) cc_final: 0.7628 (t0)
REVERT: D  436 TYR cc_start: 0.7307 (t80) cc_final: 0.7096 (t80)
REVERT: D  508 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7937 (ttpt)
REVERT: D  551 ASP cc_start: 0.7009 (m-30) cc_final: 0.6316 (t70)
REVERT: E  142 LEU cc_start: 0.8824 (mt) cc_final: 0.8623 (mt)
REVERT: E  147 ILE cc_start: 0.8599 (mm) cc_final: 0.8388 (mm)
REVERT: E  193 ASN cc_start: 0.8925 (m-40) cc_final: 0.8616 (m-40)
REVERT: F  389 LYS cc_start: 0.8620 (mmtt) cc_final: 0.7685 (mptt)
REVERT: F  430 TYR cc_start: 0.8770 (m-80) cc_final: 0.8481 (m-80)
REVERT: F  463 MET cc_start: 0.6663 (ttm) cc_final: 0.6334 (ttm)
REVERT: F  487 MET cc_start: 0.5753 (tmm) cc_final: 0.5472 (tmm)
REVERT: F  551 ASP cc_start: 0.7307 (m-30) cc_final: 0.6132 (t70)
REVERT: F  570 ASP cc_start: 0.7822 (m-30) cc_final: 0.7369 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1981
  time to fit residues: 78.4927
Evaluate side-chains
  228 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0870
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 GLN
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 HIS
** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.165064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.142943 restraints weight = 19637.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.146528 restraints weight = 12780.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.149059 restraints weight = 9194.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.5192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9978  Z= 0.150
  Angle     :  0.603   8.118  13548  Z= 0.315
  Chirality :  0.047   0.265   1647
  Planarity :  0.004   0.044   1716
  Dihedral  :  5.145  19.681   1377
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.23), residues: 1281
  helix:  0.99 (0.29), residues: 324
  sheet: -1.67 (0.45), residues: 117
  loop : -1.47 (0.22), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 423 
 HIS   0.002   0.000   HIS E 138 
 PHE   0.008   0.001   PHE F 526 
 TYR   0.015   0.001   TYR D 322 
 ARG   0.005   0.000   ARG B 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
  289 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8616 (mm) cc_final: 0.8403 (mm)
REVERT: A  164 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7783 (mm-40)
REVERT: A  193 ASN cc_start: 0.8604 (m-40) cc_final: 0.8247 (m-40)
REVERT: A  204 THR cc_start: 0.7498 (p) cc_final: 0.7125 (p)
REVERT: B  314 LEU cc_start: 0.9156 (mt) cc_final: 0.8931 (mt)
REVERT: B  335 ASP cc_start: 0.8313 (t0) cc_final: 0.7997 (t0)
REVERT: B  340 GLU cc_start: 0.7277 (pm20) cc_final: 0.7048 (pm20)
REVERT: B  389 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8104 (mmtp)
REVERT: B  510 TYR cc_start: 0.6931 (t80) cc_final: 0.6730 (t80)
REVERT: B  567 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5995 (mm-30)
REVERT: C  193 ASN cc_start: 0.9008 (m-40) cc_final: 0.8565 (m-40)
REVERT: D  250 HIS cc_start: 0.6496 (t70) cc_final: 0.6287 (t70)
REVERT: D  335 ASP cc_start: 0.8270 (t0) cc_final: 0.7687 (t0)
REVERT: D  394 SER cc_start: 0.7772 (t) cc_final: 0.6574 (p)
REVERT: D  468 GLN cc_start: 0.8451 (mm110) cc_final: 0.8231 (mm-40)
REVERT: D  482 LEU cc_start: 0.7832 (mt) cc_final: 0.7435 (mp)
REVERT: D  543 GLN cc_start: 0.7337 (tt0) cc_final: 0.6849 (tp40)
REVERT: D  551 ASP cc_start: 0.6651 (m-30) cc_final: 0.6055 (t70)
REVERT: E  193 ASN cc_start: 0.8815 (m-40) cc_final: 0.8593 (m-40)
REVERT: F  385 ASP cc_start: 0.7583 (m-30) cc_final: 0.7108 (m-30)
REVERT: F  430 TYR cc_start: 0.8674 (m-80) cc_final: 0.8300 (m-80)
REVERT: F  487 MET cc_start: 0.5671 (tmm) cc_final: 0.5380 (tmm)
REVERT: F  551 ASP cc_start: 0.7230 (m-30) cc_final: 0.6219 (t70)
REVERT: F  570 ASP cc_start: 0.7556 (m-30) cc_final: 0.7056 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1967
  time to fit residues: 81.0328
Evaluate side-chains
  234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   chunk 81 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 106 optimal weight:    0.2980
   chunk 51 optimal weight:    8.9990
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
A 209 ASN
B 344 GLN
B 458 ASN
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 574 ASN
C 209 ASN
** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 193 ASN
F 468 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.158289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.135628 restraints weight = 20009.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.138930 restraints weight = 13367.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.141253 restraints weight = 9853.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.5211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9978  Z= 0.281
  Angle     :  0.737   8.852  13548  Z= 0.386
  Chirality :  0.051   0.385   1647
  Planarity :  0.004   0.045   1716
  Dihedral  :  5.707  25.580   1377
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.99 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.23), residues: 1281
  helix:  0.58 (0.29), residues: 336
  sheet: -1.73 (0.43), residues: 117
  loop : -1.59 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 423 
 HIS   0.004   0.001   HIS C 154 
 PHE   0.014   0.002   PHE D 526 
 TYR   0.023   0.002   TYR F 293 
 ARG   0.006   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
  270 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 269
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8602 (mm) cc_final: 0.8381 (mm)
REVERT: B  335 ASP cc_start: 0.8335 (t0) cc_final: 0.8054 (t0)
REVERT: B  340 GLU cc_start: 0.7293 (pm20) cc_final: 0.6982 (pm20)
REVERT: B  385 ASP cc_start: 0.7212 (m-30) cc_final: 0.6921 (m-30)
REVERT: B  389 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8224 (mmtp)
REVERT: B  487 MET cc_start: 0.5649 (tmm) cc_final: 0.5436 (tmm)
REVERT: B  510 TYR cc_start: 0.6989 (t80) cc_final: 0.6528 (t80)
REVERT: B  567 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6337 (mm-30)
REVERT: C  158 MET cc_start: 0.6554 (tpp) cc_final: 0.6311 (tpp)
REVERT: D  250 HIS cc_start: 0.6692 (t70) cc_final: 0.6492 (t70)
REVERT: D  335 ASP cc_start: 0.8266 (t0) cc_final: 0.7623 (t0)
REVERT: D  487 MET cc_start: 0.5891 (tmm) cc_final: 0.5673 (tmm)
REVERT: D  493 LEU cc_start: 0.6390 (tp) cc_final: 0.6115 (tp)
REVERT: D  508 LYS cc_start: 0.8310 (ttpt) cc_final: 0.8005 (ttpt)
REVERT: D  543 GLN cc_start: 0.7231 (tt0) cc_final: 0.6780 (tp-100)
REVERT: D  551 ASP cc_start: 0.7010 (m-30) cc_final: 0.6206 (t70)
REVERT: F  305 MET cc_start: 0.2864 (mpp) cc_final: 0.2215 (mtm)
REVERT: F  389 LYS cc_start: 0.8661 (mmtt) cc_final: 0.7846 (mptt)
REVERT: F  429 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7268 (tpt90)
REVERT: F  430 TYR cc_start: 0.8953 (m-80) cc_final: 0.8704 (m-80)
REVERT: F  487 MET cc_start: 0.6018 (tmm) cc_final: 0.5518 (tmm)
REVERT: F  551 ASP cc_start: 0.7360 (m-30) cc_final: 0.6116 (t70)
REVERT: F  570 ASP cc_start: 0.7664 (m-30) cc_final: 0.7289 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 270
  average time/residue: 0.1894
  time to fit residues: 73.2253
Evaluate side-chains
  223 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 81 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0670
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.8720

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

Flipped N/Q/H residues before XYZ refinement:
A 138 HIS
A 209 ASN
B 257 GLN
B 344 GLN
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 574 ASN
C 138 HIS
C 193 ASN
D 574 ASN
** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.163586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.140877 restraints weight = 19954.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.144280 restraints weight = 13158.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.146654 restraints weight = 9585.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9978  Z= 0.171
  Angle     :  0.673   8.963  13548  Z= 0.353
  Chirality :  0.048   0.292   1647
  Planarity :  0.004   0.043   1716
  Dihedral  :  5.360  22.307   1377
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.23), residues: 1281
  helix:  0.61 (0.29), residues: 336
  sheet: -1.54 (0.45), residues: 117
  loop : -1.49 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 423 
 HIS   0.004   0.000   HIS E 138 
 PHE   0.011   0.001   PHE D 441 
 TYR   0.023   0.001   TYR F 322 
 ARG   0.006   0.001   ARG F 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2820.21 seconds
wall clock time: 51 minutes 42.12 seconds (3102.12 seconds total)