Starting phenix.real_space_refine
on Wed Mar  4 09:00:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6q0x_20555/03_2026/6q0x_20555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6q0x_20555/03_2026/6q0x_20555.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6q0x_20555/03_2026/6q0x_20555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6q0x_20555/03_2026/6q0x_20555.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6q0x_20555/03_2026/6q0x_20555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6q0x_20555/03_2026/6q0x_20555.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      48      5.16       5
     C    7984      2.51       5
     N    2172      2.21       5
     O    2264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12468
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 3117
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 12, 'TRANS': 360}
    Chain: "B"
      Number of atoms: 3117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 3117
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 12, 'TRANS': 360}
    Chain: "C"
      Number of atoms: 3117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 3117
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 12, 'TRANS': 360}
    Chain: "D"
      Number of atoms: 3117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 3117
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 12, 'TRANS': 360}
  Time building chain proxies: 2.54, per 1000 atoms: 0.20
  Number of scatterers: 12468
  At special positions: 0
  Unit cell: (81.312, 87.648, 184.8, 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      48     16.00
     O    2264      8.00
     N    2172      7.00
     C    7984      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 1.22
  Conformation dependent library (CDL) restraints added in 577.3 milliseconds
  

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2928

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      73.5% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 173 through 187
    Processing helix  chain 'A' and resid 207 through 227
      removed outlier: 4.296A  pdb=" N   ARG A 213 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 4.098A  pdb=" N   LEU A 237 " --> pdb=" O   ASP A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 252
    Processing helix  chain 'A' and resid 254 through 258
      removed outlier: 3.648A  pdb=" N   THR A 257 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 330
      removed outlier: 3.991A  pdb=" N   SER A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ASP A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 421
      removed outlier: 3.712A  pdb=" N   ASP A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
      Proline residue:  A 377  - end of helix
      removed outlier: 4.809A  pdb=" N   PHE A 382 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ASN A 402 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ASN A 403 " --> pdb=" O   MET A 399 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 501
      removed outlier: 3.963A  pdb=" N   CYS A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE A 466 " --> pdb=" O   GLU A 462 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   PHE A 472 " --> pdb=" O   GLN A 468 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR A 475 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 187
    Processing helix  chain 'B' and resid 207 through 227
      removed outlier: 4.296A  pdb=" N   ARG B 213 " --> pdb=" O   PHE B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 233 through 241
      removed outlier: 4.098A  pdb=" N   LEU B 237 " --> pdb=" O   ASP B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 252
    Processing helix  chain 'B' and resid 254 through 258
      removed outlier: 3.648A  pdb=" N   THR B 257 " --> pdb=" O   THR B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 330
      removed outlier: 3.991A  pdb=" N   SER B 287 " --> pdb=" O   ASN B 283 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ASP B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 421
      removed outlier: 3.711A  pdb=" N   ASP B 345 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
      Proline residue:  B 377  - end of helix
      removed outlier: 4.809A  pdb=" N   PHE B 382 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ASN B 402 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN B 403 " --> pdb=" O   MET B 399 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 501
      removed outlier: 3.964A  pdb=" N   CYS B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE B 466 " --> pdb=" O   GLU B 462 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE B 472 " --> pdb=" O   GLN B 468 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR B 475 " --> pdb=" O   GLN B 471 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR B 501 " --> pdb=" O   GLU B 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 187
    Processing helix  chain 'C' and resid 207 through 227
      removed outlier: 4.295A  pdb=" N   ARG C 213 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 233
    Processing helix  chain 'C' and resid 233 through 241
      removed outlier: 4.098A  pdb=" N   LEU C 237 " --> pdb=" O   ASP C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 252
    Processing helix  chain 'C' and resid 254 through 258
      removed outlier: 3.648A  pdb=" N   THR C 257 " --> pdb=" O   THR C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 330
      removed outlier: 3.990A  pdb=" N   SER C 287 " --> pdb=" O   ASN C 283 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ASP C 290 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 421
      removed outlier: 3.712A  pdb=" N   ASP C 345 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER C 351 " --> pdb=" O   ASN C 347 " (cutoff:3.500A)
      Proline residue:  C 377  - end of helix
      removed outlier: 4.809A  pdb=" N   PHE C 382 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR C 383 " --> pdb=" O   PHE C 379 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ASN C 402 " --> pdb=" O   ILE C 398 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ASN C 403 " --> pdb=" O   MET C 399 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET C 421 " --> pdb=" O   LYS C 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 501
      removed outlier: 3.965A  pdb=" N   CYS C 459 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE C 466 " --> pdb=" O   GLU C 462 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   PHE C 472 " --> pdb=" O   GLN C 468 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR C 475 " --> pdb=" O   GLN C 471 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR C 501 " --> pdb=" O   GLU C 497 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 187
    Processing helix  chain 'D' and resid 207 through 227
      removed outlier: 4.295A  pdb=" N   ARG D 213 " --> pdb=" O   PHE D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 233
    Processing helix  chain 'D' and resid 233 through 241
      removed outlier: 4.098A  pdb=" N   LEU D 237 " --> pdb=" O   ASP D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 252
    Processing helix  chain 'D' and resid 254 through 258
      removed outlier: 3.648A  pdb=" N   THR D 257 " --> pdb=" O   THR D 254 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 330
      removed outlier: 3.991A  pdb=" N   SER D 287 " --> pdb=" O   ASN D 283 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ASP D 290 " --> pdb=" O   ALA D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 341 through 421
      removed outlier: 3.712A  pdb=" N   ASP D 345 " --> pdb=" O   ASP D 341 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER D 351 " --> pdb=" O   ASN D 347 " (cutoff:3.500A)
      Proline residue:  D 377  - end of helix
      removed outlier: 4.809A  pdb=" N   PHE D 382 " --> pdb=" O   LYS D 378 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR D 383 " --> pdb=" O   PHE D 379 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ASN D 402 " --> pdb=" O   ILE D 398 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ASN D 403 " --> pdb=" O   MET D 399 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET D 421 " --> pdb=" O   LYS D 417 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 428 through 501
      removed outlier: 3.963A  pdb=" N   CYS D 459 " --> pdb=" O   LEU D 455 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE D 466 " --> pdb=" O   GLU D 462 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   PHE D 472 " --> pdb=" O   GLN D 468 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR D 475 " --> pdb=" O   GLN D 471 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR D 501 " --> pdb=" O   GLU D 497 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 137
      removed outlier: 6.000A  pdb=" N   ILE A 133 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LYS A 153 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLU A 135 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU A 151 " --> pdb=" O   GLU A 135 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 132 through 137
      removed outlier: 6.000A  pdb=" N   ILE B 133 " --> pdb=" O   LYS B 153 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LYS B 153 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLU B 135 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU B 151 " --> pdb=" O   GLU B 135 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 132 through 137
      removed outlier: 6.001A  pdb=" N   ILE C 133 " --> pdb=" O   LYS C 153 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LYS C 153 " --> pdb=" O   ILE C 133 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLU C 135 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU C 151 " --> pdb=" O   GLU C 135 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 137
      removed outlier: 6.001A  pdb=" N   ILE D 133 " --> pdb=" O   LYS D 153 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   LYS D 153 " --> pdb=" O   ILE D 133 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLU D 135 " --> pdb=" O   LEU D 151 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   LEU D 151 " --> pdb=" O   GLU D 135 " (cutoff:3.500A)

    900 hydrogen bonds defined for protein.
    2676 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 1.61 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: 4050
        1.34 -     1.46: 2433
        1.46 -     1.58: 6149
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 12716
  Sorted by residual:
  bond pdb=" CB  GLU A 307 "
       pdb=" CG  GLU A 307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.50e+00
  bond pdb=" CB  GLU B 307 "
       pdb=" CG  GLU B 307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.49e+00
  bond pdb=" CB  GLU D 307 "
       pdb=" CG  GLU D 307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.47e+00
  bond pdb=" CB  GLU C 307 "
       pdb=" CG  GLU C 307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.44e+00
  bond pdb=" CB  VAL B 314 "
       pdb=" CG1 VAL B 314 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.22e+00
  ... (remaining 12711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 16406
        1.84 -     3.68: 586
        3.68 -     5.52: 106
        5.52 -     7.36: 30
        7.36 -     9.20: 8
  Bond angle restraints: 17136
  Sorted by residual:
  angle pdb=" C   GLU B 165 "
        pdb=" N   GLU B 166 "
        pdb=" CA  GLU B 166 "
      ideal   model   delta    sigma   weight residual
     121.54  130.50   -8.96 1.91e+00 2.74e-01 2.20e+01
  angle pdb=" C   GLU C 165 "
        pdb=" N   GLU C 166 "
        pdb=" CA  GLU C 166 "
      ideal   model   delta    sigma   weight residual
     121.54  130.49   -8.95 1.91e+00 2.74e-01 2.20e+01
  angle pdb=" C   GLU A 165 "
        pdb=" N   GLU A 166 "
        pdb=" CA  GLU A 166 "
      ideal   model   delta    sigma   weight residual
     121.54  130.49   -8.95 1.91e+00 2.74e-01 2.19e+01
  angle pdb=" C   GLU D 165 "
        pdb=" N   GLU D 166 "
        pdb=" CA  GLU D 166 "
      ideal   model   delta    sigma   weight residual
     121.54  130.46   -8.92 1.91e+00 2.74e-01 2.18e+01
  angle pdb=" N   THR D 161 "
        pdb=" CA  THR D 161 "
        pdb=" C   THR D 161 "
      ideal   model   delta    sigma   weight residual
     109.46  102.91    6.55 1.66e+00 3.63e-01 1.56e+01
  ... (remaining 17131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6677
       17.91 -    35.81: 964
       35.81 -    53.72: 147
       53.72 -    71.63: 24
       71.63 -    89.53: 32
  Dihedral angle restraints: 7844
    sinusoidal: 3396
      harmonic: 4448
  Sorted by residual:
  dihedral pdb=" CA  SER B 160 "
           pdb=" C   SER B 160 "
           pdb=" N   THR B 161 "
           pdb=" CA  THR B 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.54   30.46     0      5.00e+00 4.00e-02 3.71e+01
  dihedral pdb=" CA  SER C 160 "
           pdb=" C   SER C 160 "
           pdb=" N   THR C 161 "
           pdb=" CA  THR C 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.55   30.45     0      5.00e+00 4.00e-02 3.71e+01
  dihedral pdb=" CA  SER A 160 "
           pdb=" C   SER A 160 "
           pdb=" N   THR A 161 "
           pdb=" CA  THR A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.60   30.40     0      5.00e+00 4.00e-02 3.70e+01
  ... (remaining 7841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1049
       0.032 -    0.064: 561
       0.064 -    0.096: 226
       0.096 -    0.128: 69
       0.128 -    0.160: 11
  Chirality restraints: 1916
  Sorted by residual:
  chirality pdb=" CA  TRP C 282 "
            pdb=" N   TRP C 282 "
            pdb=" C   TRP C 282 "
            pdb=" CB  TRP C 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  TRP D 282 "
            pdb=" N   TRP D 282 "
            pdb=" C   TRP D 282 "
            pdb=" CB  TRP D 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.42e-01
  chirality pdb=" CA  TRP B 282 "
            pdb=" N   TRP B 282 "
            pdb=" C   TRP B 282 "
            pdb=" CB  TRP B 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.03e-01
  ... (remaining 1913 not shown)

  Planarity restraints: 2160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 368 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.75e+00
        pdb=" C   THR B 368 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR B 368 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU B 369 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 368 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.74e+00
        pdb=" C   THR D 368 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR D 368 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU D 369 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 368 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.69e+00
        pdb=" C   THR A 368 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR A 368 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A 369 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2157 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 441
        2.69 -     3.24: 14469
        3.24 -     3.80: 21173
        3.80 -     4.35: 26479
        4.35 -     4.90: 40579
  Nonbonded interactions: 103141
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 335 "
            pdb=" OG1 THR D 470 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" NH1 ARG D 186 "
            pdb=" O   ASN D 259 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" NH1 ARG C 186 "
            pdb=" O   ASN C 259 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" NH1 ARG A 186 "
            pdb=" O   ASN A 259 "
     model   vdw
     2.141 3.120
  nonbonded pdb=" NH1 ARG B 186 "
            pdb=" O   ASN B 259 "
     model   vdw
     2.141 3.120
  ... (remaining 103136 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             1.020
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.770
  Find NCS groups from input model:        0.050
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
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      :  0.007   0.055  12716  Z= 0.329
  Angle     :  0.879   9.204  17136  Z= 0.496
  Chirality :  0.045   0.160   1916
  Planarity :  0.005   0.032   2160
  Dihedral  : 17.073  89.531   4916
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 24.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.79 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.83 (0.17), residues: 1484
  helix: -2.03 (0.12), residues: 1032
  sheet:  None (None), residues: 0
  loop : -3.45 (0.25), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 186 
 TYR   0.015   0.002   TYR B 297 
 PHE   0.025   0.002   PHE D 467 
 TRP   0.019   0.002   TRP B 249 
 HIS   0.006   0.002   HIS D 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 (12716)
  covalent geometry    : angle       0.87873 (17136)
  hydrogen bonds       : bond        0.11296 (  900)
  hydrogen bonds       : angle       6.35351 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  444 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 427
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A  224 VAL cc_start: 0.9290 (t) cc_final: 0.8839 (t)
REVERT: A  225 MET cc_start: 0.7569 (mmm) cc_final: 0.7342 (tpp)
REVERT: A  226 LYS cc_start: 0.4613 (tptm) cc_final: 0.3675 (tptp)
REVERT: A  260 GLU cc_start: 0.7171 (tp30) cc_final: 0.6415 (tm-30)
REVERT: A  294 GLU cc_start: 0.7548 (tt0) cc_final: 0.7148 (tt0)
REVERT: A  306 HIS cc_start: 0.8065 (m-70) cc_final: 0.7851 (m-70)
REVERT: A  330 VAL cc_start: 0.8236 (m) cc_final: 0.7990 (m)
REVERT: A  337 VAL cc_start: 0.8430 (m) cc_final: 0.8193 (p)
REVERT: A  375 LEU cc_start: 0.8530 (tt) cc_final: 0.8013 (tt)
REVERT: A  392 LEU cc_start: 0.8730 (mt) cc_final: 0.8254 (tt)
REVERT: A  393 PHE cc_start: 0.7975 (m-10) cc_final: 0.7757 (m-80)
REVERT: A  409 ARG cc_start: 0.7806 (ttt180) cc_final: 0.7496 (ttt180)
REVERT: B  224 VAL cc_start: 0.9286 (t) cc_final: 0.8686 (t)
REVERT: B  226 LYS cc_start: 0.4639 (tptm) cc_final: 0.4405 (tptt)
REVERT: B  321 GLU cc_start: 0.7865 (tt0) cc_final: 0.7657 (tt0)
REVERT: B  330 VAL cc_start: 0.8158 (m) cc_final: 0.7903 (m)
REVERT: B  337 VAL cc_start: 0.8396 (m) cc_final: 0.8095 (p)
REVERT: B  347 ASN cc_start: 0.8457 (p0) cc_final: 0.7969 (p0)
REVERT: B  375 LEU cc_start: 0.8487 (tt) cc_final: 0.7973 (tt)
REVERT: B  392 LEU cc_start: 0.8729 (mt) cc_final: 0.8201 (tt)
REVERT: B  409 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7536 (ttt180)
REVERT: C  224 VAL cc_start: 0.9292 (t) cc_final: 0.8899 (t)
REVERT: C  225 MET cc_start: 0.7554 (mmm) cc_final: 0.7314 (tpp)
REVERT: C  226 LYS cc_start: 0.4770 (tptm) cc_final: 0.3793 (tptp)
REVERT: C  260 GLU cc_start: 0.7356 (tp30) cc_final: 0.6550 (tm-30)
REVERT: C  306 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7813 (m-70)
REVERT: C  307 GLU cc_start: 0.7062 (tp30) cc_final: 0.6846 (tp30)
REVERT: C  330 VAL cc_start: 0.8237 (m) cc_final: 0.7998 (m)
REVERT: C  337 VAL cc_start: 0.8410 (m) cc_final: 0.8146 (p)
REVERT: C  375 LEU cc_start: 0.8497 (tt) cc_final: 0.7971 (tt)
REVERT: C  392 LEU cc_start: 0.8760 (mt) cc_final: 0.8266 (tt)
REVERT: C  393 PHE cc_start: 0.7964 (m-10) cc_final: 0.7744 (m-80)
REVERT: C  409 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7520 (ttt180)
REVERT: D  224 VAL cc_start: 0.9289 (t) cc_final: 0.8646 (t)
REVERT: D  226 LYS cc_start: 0.4644 (tptm) cc_final: 0.4292 (tptt)
REVERT: D  260 GLU cc_start: 0.7058 (tp30) cc_final: 0.6330 (tm-30)
REVERT: D  330 VAL cc_start: 0.8269 (m) cc_final: 0.8014 (m)
REVERT: D  337 VAL cc_start: 0.8428 (m) cc_final: 0.8122 (p)
REVERT: D  375 LEU cc_start: 0.8526 (tt) cc_final: 0.8025 (tt)
REVERT: D  392 LEU cc_start: 0.8748 (mt) cc_final: 0.8248 (tt)
REVERT: D  393 PHE cc_start: 0.7970 (m-10) cc_final: 0.7761 (m-80)
REVERT: D  409 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7465 (ttt180)
  outliers start: 17
  outliers final: 0
  residues processed: 439
  average time/residue: 0.1163
  time to fit residues: 71.5056
Evaluate side-chains
  291 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 290
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0070
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0770
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.3156

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
A 306 HIS
** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 HIS
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 306 HIS
** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.177724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.145128 restraints weight = 25256.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.148773 restraints weight = 15508.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.151161 restraints weight = 11027.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.152896 restraints weight = 8786.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.153789 restraints weight = 7464.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12716  Z= 0.192
  Angle     :  0.759   8.449  17136  Z= 0.394
  Chirality :  0.045   0.189   1916
  Planarity :  0.005   0.045   2160
  Dihedral  :  5.987  28.400   1624
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.29 %
    Favored  : 94.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.21), residues: 1484
  helix: -0.31 (0.15), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.55 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 186 
 TYR   0.011   0.002   TYR D 173 
 PHE   0.028   0.003   PHE C 220 
 TRP   0.027   0.003   TRP B 282 
 HIS   0.011   0.003   HIS D 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (12716)
  covalent geometry    : angle       0.75942 (17136)
  hydrogen bonds       : bond        0.06863 (  900)
  hydrogen bonds       : angle       5.22768 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 388
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A  153 LYS cc_start: 0.8745 (tptp) cc_final: 0.8362 (tptp)
REVERT: A  226 LYS cc_start: 0.4077 (tptm) cc_final: 0.3117 (mtmm)
REVERT: A  244 THR cc_start: 0.7716 (t) cc_final: 0.7368 (t)
REVERT: A  270 PHE cc_start: 0.7694 (t80) cc_final: 0.6988 (m-80)
REVERT: A  312 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: A  337 VAL cc_start: 0.8762 (m) cc_final: 0.8478 (p)
REVERT: A  392 LEU cc_start: 0.8635 (mt) cc_final: 0.8134 (tt)
REVERT: A  394 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: A  399 MET cc_start: 0.8472 (tpp) cc_final: 0.8193 (tpp)
REVERT: A  485 ASN cc_start: 0.8654 (t0) cc_final: 0.8234 (t0)
REVERT: B  153 LYS cc_start: 0.8819 (tptp) cc_final: 0.8448 (tptp)
REVERT: B  227 HIS cc_start: 0.7632 (m90) cc_final: 0.7416 (m90)
REVERT: B  244 THR cc_start: 0.7741 (t) cc_final: 0.7367 (t)
REVERT: B  270 PHE cc_start: 0.7845 (t80) cc_final: 0.7181 (m-80)
REVERT: B  312 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: B  337 VAL cc_start: 0.8774 (m) cc_final: 0.8488 (p)
REVERT: B  392 LEU cc_start: 0.8558 (mt) cc_final: 0.8063 (tt)
REVERT: B  394 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: C  153 LYS cc_start: 0.8797 (tptp) cc_final: 0.8386 (tptp)
REVERT: C  175 ASP cc_start: 0.8178 (m-30) cc_final: 0.7930 (m-30)
REVERT: C  181 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8639 (mm-30)
REVERT: C  224 VAL cc_start: 0.9067 (t) cc_final: 0.8679 (t)
REVERT: C  227 HIS cc_start: 0.7202 (m170) cc_final: 0.6660 (m90)
REVERT: C  244 THR cc_start: 0.7731 (t) cc_final: 0.7398 (t)
REVERT: C  270 PHE cc_start: 0.7626 (t80) cc_final: 0.6944 (m-80)
REVERT: C  312 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: C  337 VAL cc_start: 0.8787 (m) cc_final: 0.8483 (p)
REVERT: C  392 LEU cc_start: 0.8637 (mt) cc_final: 0.8160 (tt)
REVERT: C  394 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7933 (mt-10)
REVERT: C  485 ASN cc_start: 0.8684 (t0) cc_final: 0.8208 (t0)
REVERT: D  153 LYS cc_start: 0.8768 (tptp) cc_final: 0.8376 (tptp)
REVERT: D  244 THR cc_start: 0.7735 (t) cc_final: 0.7366 (t)
REVERT: D  270 PHE cc_start: 0.7730 (t80) cc_final: 0.7102 (m-80)
REVERT: D  309 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7839 (ttm-80)
REVERT: D  312 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7482 (tm-30)
REVERT: D  337 VAL cc_start: 0.8806 (m) cc_final: 0.8526 (p)
REVERT: D  392 LEU cc_start: 0.8623 (mt) cc_final: 0.8137 (tt)
REVERT: D  394 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7807 (mt-10)
REVERT: D  399 MET cc_start: 0.8477 (tpp) cc_final: 0.8222 (tpp)
REVERT: D  485 ASN cc_start: 0.8666 (t0) cc_final: 0.8192 (t0)
  outliers start: 8
  outliers final: 0
  residues processed: 392
  average time/residue: 0.1147
  time to fit residues: 63.7361
Evaluate side-chains
  300 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 281 GLN
A 449 GLN
** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
B 339 GLN
C 281 GLN
C 339 GLN
C 449 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 259 ASN
D 281 GLN
D 449 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.176191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.143238 restraints weight = 25599.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.146712 restraints weight = 16512.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.149197 restraints weight = 11986.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.150862 restraints weight = 9464.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.151978 restraints weight = 8041.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12716  Z= 0.177
  Angle     :  0.672   6.723  17136  Z= 0.364
  Chirality :  0.042   0.144   1916
  Planarity :  0.004   0.039   2160
  Dihedral  :  5.687  26.832   1624
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 18.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  4.57 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.22), residues: 1484
  helix:  0.25 (0.16), residues: 1072
  sheet:  None (None), residues: 0
  loop : -2.42 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 172 
 TYR   0.014   0.001   TYR D 150 
 PHE   0.035   0.002   PHE B 220 
 TRP   0.027   0.002   TRP B 282 
 HIS   0.010   0.002   HIS A 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12716)
  covalent geometry    : angle       0.67237 (17136)
  hydrogen bonds       : bond        0.06449 (  900)
  hydrogen bonds       : angle       4.99510 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 356
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  153 LYS cc_start: 0.8747 (tptp) cc_final: 0.8449 (tptp)
REVERT: A  224 VAL cc_start: 0.8956 (t) cc_final: 0.8745 (t)
REVERT: A  270 PHE cc_start: 0.7593 (t80) cc_final: 0.6859 (m-80)
REVERT: A  282 TRP cc_start: 0.8425 (p90) cc_final: 0.8123 (p90)
REVERT: A  312 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: A  384 ASP cc_start: 0.8009 (m-30) cc_final: 0.7364 (t70)
REVERT: A  399 MET cc_start: 0.8540 (tpp) cc_final: 0.8286 (tpp)
REVERT: A  485 ASN cc_start: 0.8718 (t0) cc_final: 0.8339 (t0)
REVERT: B  153 LYS cc_start: 0.8820 (tptp) cc_final: 0.8501 (tptp)
REVERT: B  270 PHE cc_start: 0.7674 (t80) cc_final: 0.6906 (m-80)
REVERT: B  293 MET cc_start: 0.8812 (tpp) cc_final: 0.8295 (tmm)
REVERT: B  311 MET cc_start: 0.7336 (tpt) cc_final: 0.7090 (tpt)
REVERT: B  357 LEU cc_start: 0.9263 (mt) cc_final: 0.8891 (mt)
REVERT: B  394 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7837 (mt-10)
REVERT: B  485 ASN cc_start: 0.8862 (t0) cc_final: 0.8624 (t0)
REVERT: C  153 LYS cc_start: 0.8793 (tptp) cc_final: 0.8454 (tptp)
REVERT: C  224 VAL cc_start: 0.9068 (t) cc_final: 0.8654 (t)
REVERT: C  227 HIS cc_start: 0.7221 (m170) cc_final: 0.6753 (m90)
REVERT: C  260 GLU cc_start: 0.7109 (tp30) cc_final: 0.6170 (tm-30)
REVERT: C  270 PHE cc_start: 0.7649 (t80) cc_final: 0.6893 (m-80)
REVERT: C  282 TRP cc_start: 0.8450 (p90) cc_final: 0.8125 (p90)
REVERT: C  312 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: C  357 LEU cc_start: 0.9239 (mt) cc_final: 0.8862 (mt)
REVERT: C  384 ASP cc_start: 0.8106 (m-30) cc_final: 0.7424 (t70)
REVERT: C  392 LEU cc_start: 0.8687 (mt) cc_final: 0.8172 (tt)
REVERT: C  394 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: C  485 ASN cc_start: 0.8776 (t0) cc_final: 0.8377 (t0)
REVERT: D  153 LYS cc_start: 0.8779 (tptp) cc_final: 0.8462 (tptp)
REVERT: D  181 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8568 (mm-30)
REVERT: D  213 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7498 (tpp80)
REVERT: D  226 LYS cc_start: 0.4731 (tptt) cc_final: 0.4217 (tptp)
REVERT: D  270 PHE cc_start: 0.7692 (t80) cc_final: 0.6919 (m-80)
REVERT: D  282 TRP cc_start: 0.8460 (p90) cc_final: 0.8166 (p90)
REVERT: D  311 MET cc_start: 0.7516 (tpt) cc_final: 0.7267 (tpt)
REVERT: D  357 LEU cc_start: 0.9130 (mm) cc_final: 0.8741 (mm)
REVERT: D  384 ASP cc_start: 0.8067 (m-30) cc_final: 0.7406 (t70)
REVERT: D  399 MET cc_start: 0.8539 (tpp) cc_final: 0.8253 (tpp)
REVERT: D  485 ASN cc_start: 0.8762 (t0) cc_final: 0.8348 (t0)
  outliers start: 11
  outliers final: 0
  residues processed: 360
  average time/residue: 0.1221
  time to fit residues: 61.3665
Evaluate side-chains
  266 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   chunk 133 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 144 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   chunk 118 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
A 449 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 ASN
B 281 GLN
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 GLN
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 ASN
C 281 GLN
C 339 GLN
C 449 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 449 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.175643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.145209 restraints weight = 25445.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.148045 restraints weight = 17171.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.150027 restraints weight = 12900.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.151310 restraints weight = 10546.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.151966 restraints weight = 9206.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12716  Z= 0.179
  Angle     :  0.665   7.174  17136  Z= 0.355
  Chirality :  0.042   0.174   1916
  Planarity :  0.005   0.043   2160
  Dihedral  :  5.610  25.782   1624
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.50 %
    Favored  : 94.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.22), residues: 1484
  helix:  0.58 (0.16), residues: 1072
  sheet:  None (None), residues: 0
  loop : -2.36 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 213 
 TYR   0.009   0.001   TYR D 150 
 PHE   0.041   0.002   PHE B 220 
 TRP   0.020   0.002   TRP B 282 
 HIS   0.011   0.002   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (12716)
  covalent geometry    : angle       0.66499 (17136)
  hydrogen bonds       : bond        0.06219 (  900)
  hydrogen bonds       : angle       4.90568 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 346
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 LEU cc_start: 0.9001 (mm) cc_final: 0.8670 (mm)
REVERT: A  384 ASP cc_start: 0.8062 (m-30) cc_final: 0.7626 (t70)
REVERT: A  394 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: A  399 MET cc_start: 0.8403 (tpp) cc_final: 0.8165 (tpp)
REVERT: A  485 ASN cc_start: 0.8761 (t0) cc_final: 0.8543 (t0)
REVERT: B  213 ARG cc_start: 0.8023 (ttt180) cc_final: 0.7555 (ttt180)
REVERT: B  270 PHE cc_start: 0.7757 (t80) cc_final: 0.6976 (m-80)
REVERT: B  368 THR cc_start: 0.8604 (p) cc_final: 0.8154 (p)
REVERT: B  394 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: C  224 VAL cc_start: 0.9149 (t) cc_final: 0.8658 (t)
REVERT: C  227 HIS cc_start: 0.7038 (m170) cc_final: 0.6766 (m90)
REVERT: C  260 GLU cc_start: 0.7245 (tp30) cc_final: 0.6308 (tm-30)
REVERT: C  270 PHE cc_start: 0.7720 (t80) cc_final: 0.6874 (m-80)
REVERT: C  357 LEU cc_start: 0.9236 (mt) cc_final: 0.8818 (mt)
REVERT: C  384 ASP cc_start: 0.8102 (m-30) cc_final: 0.7549 (t70)
REVERT: C  485 ASN cc_start: 0.8659 (t0) cc_final: 0.8352 (t0)
REVERT: D  226 LYS cc_start: 0.5151 (tptt) cc_final: 0.3955 (mtmm)
REVERT: D  270 PHE cc_start: 0.7706 (t80) cc_final: 0.6907 (m-80)
REVERT: D  357 LEU cc_start: 0.9055 (mm) cc_final: 0.8386 (mm)
REVERT: D  384 ASP cc_start: 0.7991 (m-30) cc_final: 0.7526 (t70)
REVERT: D  394 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: D  399 MET cc_start: 0.8439 (tpp) cc_final: 0.8151 (tpp)
REVERT: D  485 ASN cc_start: 0.8679 (t0) cc_final: 0.8399 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1201
  time to fit residues: 58.2763
Evaluate side-chains
  280 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 118 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 134 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0870
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
A 449 GLN
B 281 GLN
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 GLN
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 449 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 449 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.172165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.141380 restraints weight = 25735.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.144557 restraints weight = 16502.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.146741 restraints weight = 12008.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.148160 restraints weight = 9602.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.148913 restraints weight = 8266.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  12716  Z= 0.251
  Angle     :  0.760   7.589  17136  Z= 0.405
  Chirality :  0.044   0.164   1916
  Planarity :  0.005   0.073   2160
  Dihedral  :  5.684  26.267   1624
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 19.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.57 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.22), residues: 1484
  helix:  0.50 (0.15), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.49 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 309 
 TYR   0.011   0.002   TYR D 297 
 PHE   0.042   0.003   PHE B 220 
 TRP   0.055   0.004   TRP B 282 
 HIS   0.012   0.002   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 (12716)
  covalent geometry    : angle       0.75985 (17136)
  hydrogen bonds       : bond        0.06443 (  900)
  hydrogen bonds       : angle       5.16030 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 341
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 VAL cc_start: 0.9257 (t) cc_final: 0.8873 (t)
REVERT: A  357 LEU cc_start: 0.9111 (mm) cc_final: 0.8573 (mm)
REVERT: A  368 THR cc_start: 0.8684 (p) cc_final: 0.8142 (p)
REVERT: A  384 ASP cc_start: 0.8204 (m-30) cc_final: 0.7691 (t70)
REVERT: A  399 MET cc_start: 0.8472 (tpp) cc_final: 0.7932 (tpp)
REVERT: A  485 ASN cc_start: 0.8751 (t0) cc_final: 0.8481 (t0)
REVERT: B  153 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8383 (tptp)
REVERT: B  311 MET cc_start: 0.7447 (tpt) cc_final: 0.6895 (tpt)
REVERT: B  321 GLU cc_start: 0.8508 (tt0) cc_final: 0.7167 (tt0)
REVERT: B  358 GLU cc_start: 0.8315 (tp30) cc_final: 0.8043 (tp30)
REVERT: B  394 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7805 (mt-10)
REVERT: B  399 MET cc_start: 0.8751 (tpp) cc_final: 0.8519 (tpp)
REVERT: B  421 MET cc_start: 0.6051 (tpt) cc_final: 0.5594 (ppp)
REVERT: C  213 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7627 (ttt180)
REVERT: C  224 VAL cc_start: 0.9144 (t) cc_final: 0.8662 (t)
REVERT: C  227 HIS cc_start: 0.7076 (m170) cc_final: 0.6804 (m90)
REVERT: C  260 GLU cc_start: 0.7332 (tp30) cc_final: 0.6355 (tm-30)
REVERT: C  294 GLU cc_start: 0.8219 (tt0) cc_final: 0.7865 (tt0)
REVERT: C  357 LEU cc_start: 0.9200 (mt) cc_final: 0.8845 (mt)
REVERT: C  384 ASP cc_start: 0.8256 (m-30) cc_final: 0.7685 (t70)
REVERT: C  485 ASN cc_start: 0.8722 (t0) cc_final: 0.8416 (t0)
REVERT: D  153 LYS cc_start: 0.8634 (tmtt) cc_final: 0.8327 (tptp)
REVERT: D  224 VAL cc_start: 0.9279 (t) cc_final: 0.8985 (t)
REVERT: D  307 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7468 (tp30)
REVERT: D  357 LEU cc_start: 0.9110 (mm) cc_final: 0.8310 (mm)
REVERT: D  368 THR cc_start: 0.8642 (p) cc_final: 0.8423 (p)
REVERT: D  384 ASP cc_start: 0.8233 (m-30) cc_final: 0.7652 (t70)
REVERT: D  394 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7777 (mt-10)
REVERT: D  485 ASN cc_start: 0.8706 (t0) cc_final: 0.8406 (t0)
  outliers start: 5
  outliers final: 0
  residues processed: 341
  average time/residue: 0.1157
  time to fit residues: 56.9028
Evaluate side-chains
  268 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 135 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 131 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 122 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 449 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.175801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.144521 restraints weight = 25708.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.147399 restraints weight = 17598.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.149473 restraints weight = 13359.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.150706 restraints weight = 10940.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.151710 restraints weight = 9595.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.4309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12716  Z= 0.165
  Angle     :  0.685   6.776  17136  Z= 0.362
  Chirality :  0.043   0.196   1916
  Planarity :  0.005   0.085   2160
  Dihedral  :  5.514  25.464   1624
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.57 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.23), residues: 1484
  helix:  0.78 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.30 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 172 
 TYR   0.026   0.002   TYR D 173 
 PHE   0.043   0.002   PHE B 220 
 TRP   0.074   0.003   TRP B 282 
 HIS   0.019   0.002   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12716)
  covalent geometry    : angle       0.68460 (17136)
  hydrogen bonds       : bond        0.06191 (  900)
  hydrogen bonds       : angle       4.82979 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 352
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8571 (tmtt) cc_final: 0.8303 (tptp)
REVERT: A  224 VAL cc_start: 0.9247 (t) cc_final: 0.9020 (t)
REVERT: A  312 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: A  357 LEU cc_start: 0.9012 (mm) cc_final: 0.8302 (mm)
REVERT: A  384 ASP cc_start: 0.7898 (m-30) cc_final: 0.7321 (t70)
REVERT: A  399 MET cc_start: 0.8370 (tpp) cc_final: 0.7935 (tpp)
REVERT: A  421 MET cc_start: 0.6252 (tpt) cc_final: 0.5867 (ppp)
REVERT: B  153 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8353 (tptp)
REVERT: B  226 LYS cc_start: 0.5232 (tptt) cc_final: 0.3897 (mtmm)
REVERT: B  281 GLN cc_start: 0.8793 (pp30) cc_final: 0.8585 (pp30)
REVERT: B  309 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7471 (ttm-80)
REVERT: B  357 LEU cc_start: 0.9147 (mt) cc_final: 0.8787 (mt)
REVERT: B  399 MET cc_start: 0.8817 (tpp) cc_final: 0.8464 (tpp)
REVERT: B  421 MET cc_start: 0.6172 (tpt) cc_final: 0.5809 (ppp)
REVERT: C  153 LYS cc_start: 0.8570 (tmtt) cc_final: 0.8337 (tptp)
REVERT: C  224 VAL cc_start: 0.9213 (t) cc_final: 0.8758 (t)
REVERT: C  227 HIS cc_start: 0.6932 (m170) cc_final: 0.6697 (m90)
REVERT: C  312 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: C  357 LEU cc_start: 0.9171 (mt) cc_final: 0.8803 (mt)
REVERT: C  384 ASP cc_start: 0.8024 (m-30) cc_final: 0.7447 (t70)
REVERT: C  421 MET cc_start: 0.6222 (tpt) cc_final: 0.5867 (ppp)
REVERT: C  485 ASN cc_start: 0.8679 (t0) cc_final: 0.8384 (t0)
REVERT: D  153 LYS cc_start: 0.8649 (tmtt) cc_final: 0.8338 (tptp)
REVERT: D  223 LEU cc_start: 0.8673 (tp) cc_final: 0.7883 (tp)
REVERT: D  224 VAL cc_start: 0.9286 (t) cc_final: 0.9020 (t)
REVERT: D  225 MET cc_start: 0.8061 (tpp) cc_final: 0.7817 (mpp)
REVERT: D  226 LYS cc_start: 0.5006 (tptt) cc_final: 0.3801 (mtmm)
REVERT: D  307 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7195 (tp30)
REVERT: D  312 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: D  357 LEU cc_start: 0.9008 (mm) cc_final: 0.8211 (mm)
REVERT: D  368 THR cc_start: 0.8490 (p) cc_final: 0.8193 (p)
REVERT: D  384 ASP cc_start: 0.7941 (m-30) cc_final: 0.7395 (t70)
REVERT: D  421 MET cc_start: 0.6208 (tpt) cc_final: 0.5857 (ppp)
REVERT: D  485 ASN cc_start: 0.8657 (t0) cc_final: 0.8424 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 353
  average time/residue: 0.1112
  time to fit residues: 56.8342
Evaluate side-chains
  284 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 122 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 144 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
C 449 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 449 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.174612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.143402 restraints weight = 25508.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.146845 restraints weight = 16101.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.149193 restraints weight = 11619.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.150546 restraints weight = 9201.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.151823 restraints weight = 7915.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12716  Z= 0.170
  Angle     :  0.675   6.600  17136  Z= 0.359
  Chirality :  0.044   0.179   1916
  Planarity :  0.005   0.047   2160
  Dihedral  :  5.404  24.321   1624
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.07 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.22), residues: 1484
  helix:  0.78 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.36 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 172 
 TYR   0.014   0.002   TYR C 173 
 PHE   0.048   0.002   PHE B 220 
 TRP   0.075   0.003   TRP B 282 
 HIS   0.019   0.002   HIS A 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12716)
  covalent geometry    : angle       0.67473 (17136)
  hydrogen bonds       : bond        0.06035 (  900)
  hydrogen bonds       : angle       4.84012 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 347
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8570 (tmtt) cc_final: 0.8295 (tptp)
REVERT: A  223 LEU cc_start: 0.8714 (tp) cc_final: 0.7639 (tp)
REVERT: A  224 VAL cc_start: 0.9249 (t) cc_final: 0.8956 (t)
REVERT: A  312 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: A  329 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7580 (mp0)
REVERT: A  357 LEU cc_start: 0.9113 (mm) cc_final: 0.8508 (mm)
REVERT: A  384 ASP cc_start: 0.7846 (m-30) cc_final: 0.7350 (t70)
REVERT: A  399 MET cc_start: 0.8341 (tpp) cc_final: 0.7922 (tpp)
REVERT: A  421 MET cc_start: 0.6108 (tpt) cc_final: 0.5852 (ppp)
REVERT: B  153 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8357 (tptp)
REVERT: B  224 VAL cc_start: 0.9265 (t) cc_final: 0.8992 (t)
REVERT: B  311 MET cc_start: 0.7527 (tpt) cc_final: 0.7198 (tpt)
REVERT: B  312 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: B  358 GLU cc_start: 0.8338 (tp30) cc_final: 0.8060 (tp30)
REVERT: B  399 MET cc_start: 0.8837 (tpp) cc_final: 0.8445 (tpp)
REVERT: B  421 MET cc_start: 0.6027 (tpt) cc_final: 0.5770 (ppp)
REVERT: C  153 LYS cc_start: 0.8635 (tmtt) cc_final: 0.8337 (tptp)
REVERT: C  224 VAL cc_start: 0.9214 (t) cc_final: 0.8749 (t)
REVERT: C  227 HIS cc_start: 0.6984 (m170) cc_final: 0.6730 (m90)
REVERT: C  311 MET cc_start: 0.7529 (tpt) cc_final: 0.7118 (tpt)
REVERT: C  312 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: C  329 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7555 (mp0)
REVERT: C  357 LEU cc_start: 0.9197 (mt) cc_final: 0.8799 (mt)
REVERT: C  368 THR cc_start: 0.8654 (p) cc_final: 0.8136 (p)
REVERT: C  384 ASP cc_start: 0.8004 (m-30) cc_final: 0.7416 (t70)
REVERT: C  421 MET cc_start: 0.6227 (tpt) cc_final: 0.5919 (ppp)
REVERT: C  485 ASN cc_start: 0.8638 (t0) cc_final: 0.8340 (t0)
REVERT: D  153 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8346 (tptp)
REVERT: D  223 LEU cc_start: 0.8667 (tp) cc_final: 0.7547 (tp)
REVERT: D  224 VAL cc_start: 0.9266 (t) cc_final: 0.8998 (t)
REVERT: D  225 MET cc_start: 0.8015 (tpp) cc_final: 0.7698 (mpp)
REVERT: D  226 LYS cc_start: 0.4925 (tptt) cc_final: 0.4596 (tptm)
REVERT: D  329 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7584 (mp0)
REVERT: D  357 LEU cc_start: 0.9022 (mm) cc_final: 0.8623 (mm)
REVERT: D  368 THR cc_start: 0.8454 (p) cc_final: 0.8224 (p)
REVERT: D  384 ASP cc_start: 0.7995 (m-30) cc_final: 0.7447 (t70)
REVERT: D  421 MET cc_start: 0.6078 (tpt) cc_final: 0.5814 (ppp)
REVERT: D  485 ASN cc_start: 0.8699 (t0) cc_final: 0.8396 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1043
  time to fit residues: 52.8027
Evaluate side-chains
  284 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 72 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 111 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0270
   chunk 7 optimal weight:    9.9990
   chunk 116 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 129 optimal weight:    7.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
C 281 GLN
D 147 HIS
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 366 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.177234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.147141 restraints weight = 25493.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.150234 restraints weight = 16819.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.152434 restraints weight = 12426.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.153872 restraints weight = 9956.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.154931 restraints weight = 8551.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.4903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12716  Z= 0.155
  Angle     :  0.657   6.953  17136  Z= 0.348
  Chirality :  0.043   0.182   1916
  Planarity :  0.004   0.045   2160
  Dihedral  :  5.196  23.920   1624
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.50 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.22), residues: 1484
  helix:  1.00 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.35 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 172 
 TYR   0.017   0.002   TYR B 173 
 PHE   0.046   0.002   PHE B 220 
 TRP   0.072   0.003   TRP B 282 
 HIS   0.009   0.001   HIS B 356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12716)
  covalent geometry    : angle       0.65741 (17136)
  hydrogen bonds       : bond        0.05798 (  900)
  hydrogen bonds       : angle       4.63778 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 352
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8271 (tptp)
REVERT: A  187 TYR cc_start: 0.8575 (m-80) cc_final: 0.7998 (m-80)
REVERT: A  223 LEU cc_start: 0.8699 (tp) cc_final: 0.7596 (tp)
REVERT: A  224 VAL cc_start: 0.9238 (t) cc_final: 0.8983 (t)
REVERT: A  307 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7189 (tp30)
REVERT: A  312 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7893 (tm-30)
REVERT: A  356 HIS cc_start: 0.7129 (t-90) cc_final: 0.6595 (t70)
REVERT: A  368 THR cc_start: 0.8630 (p) cc_final: 0.8421 (p)
REVERT: A  384 ASP cc_start: 0.7557 (m-30) cc_final: 0.7053 (t70)
REVERT: A  399 MET cc_start: 0.8334 (tpp) cc_final: 0.7941 (tpp)
REVERT: A  421 MET cc_start: 0.6122 (tpt) cc_final: 0.5901 (ppp)
REVERT: A  499 LEU cc_start: 0.8943 (tt) cc_final: 0.8729 (tt)
REVERT: B  153 LYS cc_start: 0.8626 (tmtt) cc_final: 0.8300 (tptp)
REVERT: B  223 LEU cc_start: 0.8578 (tp) cc_final: 0.7798 (tp)
REVERT: B  226 LYS cc_start: 0.4381 (tptt) cc_final: 0.3010 (mtmm)
REVERT: B  311 MET cc_start: 0.7173 (tpt) cc_final: 0.6851 (tpt)
REVERT: B  321 GLU cc_start: 0.8344 (tt0) cc_final: 0.7117 (tt0)
REVERT: B  343 ILE cc_start: 0.8710 (mp) cc_final: 0.8483 (mt)
REVERT: B  358 GLU cc_start: 0.8166 (tp30) cc_final: 0.7882 (tp30)
REVERT: B  399 MET cc_start: 0.8768 (tpp) cc_final: 0.8378 (tpp)
REVERT: C  153 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8288 (tptp)
REVERT: C  224 VAL cc_start: 0.9120 (t) cc_final: 0.8688 (t)
REVERT: C  311 MET cc_start: 0.7295 (tpt) cc_final: 0.6891 (tpt)
REVERT: C  312 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: C  343 ILE cc_start: 0.8825 (mp) cc_final: 0.8207 (mt)
REVERT: C  384 ASP cc_start: 0.7724 (m-30) cc_final: 0.7162 (t70)
REVERT: C  421 MET cc_start: 0.6039 (tpt) cc_final: 0.5831 (ppp)
REVERT: C  485 ASN cc_start: 0.8695 (t0) cc_final: 0.8382 (t0)
REVERT: D  153 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8296 (tptp)
REVERT: D  223 LEU cc_start: 0.8617 (tp) cc_final: 0.7564 (tp)
REVERT: D  224 VAL cc_start: 0.9337 (t) cc_final: 0.9122 (t)
REVERT: D  225 MET cc_start: 0.8018 (tpp) cc_final: 0.7800 (mpp)
REVERT: D  226 LYS cc_start: 0.4851 (tptt) cc_final: 0.4405 (tptt)
REVERT: D  321 GLU cc_start: 0.8578 (tt0) cc_final: 0.7233 (tt0)
REVERT: D  357 LEU cc_start: 0.9044 (mm) cc_final: 0.8503 (mm)
REVERT: D  358 GLU cc_start: 0.8181 (tp30) cc_final: 0.7935 (tp30)
REVERT: D  368 THR cc_start: 0.8456 (p) cc_final: 0.7803 (p)
REVERT: D  384 ASP cc_start: 0.7734 (m-30) cc_final: 0.7193 (t70)
REVERT: D  485 ASN cc_start: 0.8649 (t0) cc_final: 0.8399 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 352
  average time/residue: 0.1023
  time to fit residues: 53.9935
Evaluate side-chains
  287 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 110 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0060
   chunk 136 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 125 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   overall best weight:    1.3202

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.176611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.145170 restraints weight = 25424.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.148499 restraints weight = 16484.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.150775 restraints weight = 12088.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.152380 restraints weight = 9653.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.153465 restraints weight = 8234.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.5043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12716  Z= 0.167
  Angle     :  0.686   9.998  17136  Z= 0.360
  Chirality :  0.043   0.227   1916
  Planarity :  0.004   0.034   2160
  Dihedral  :  5.187  25.444   1624
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.22), residues: 1484
  helix:  0.97 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.38 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 172 
 TYR   0.016   0.002   TYR B 173 
 PHE   0.042   0.002   PHE B 220 
 TRP   0.084   0.003   TRP B 282 
 HIS   0.025   0.002   HIS C 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12716)
  covalent geometry    : angle       0.68644 (17136)
  hydrogen bonds       : bond        0.05743 (  900)
  hydrogen bonds       : angle       4.72395 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 346
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8305 (tptp)
REVERT: A  187 TYR cc_start: 0.8556 (m-80) cc_final: 0.7988 (m-80)
REVERT: A  223 LEU cc_start: 0.8702 (tp) cc_final: 0.7599 (tp)
REVERT: A  224 VAL cc_start: 0.9305 (t) cc_final: 0.9041 (t)
REVERT: A  356 HIS cc_start: 0.7149 (t-90) cc_final: 0.6727 (t70)
REVERT: A  368 THR cc_start: 0.8541 (p) cc_final: 0.8299 (p)
REVERT: A  384 ASP cc_start: 0.7530 (m-30) cc_final: 0.7091 (t70)
REVERT: A  394 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: A  399 MET cc_start: 0.8431 (tpp) cc_final: 0.7916 (tpp)
REVERT: B  153 LYS cc_start: 0.8645 (tmtt) cc_final: 0.8311 (tptp)
REVERT: B  223 LEU cc_start: 0.8609 (tp) cc_final: 0.7808 (tp)
REVERT: B  226 LYS cc_start: 0.4373 (tptt) cc_final: 0.3202 (mtmm)
REVERT: B  321 GLU cc_start: 0.8266 (tt0) cc_final: 0.6752 (tt0)
REVERT: B  329 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7687 (mp0)
REVERT: B  358 GLU cc_start: 0.8110 (tp30) cc_final: 0.7703 (tp30)
REVERT: B  399 MET cc_start: 0.8787 (tpp) cc_final: 0.8396 (tpp)
REVERT: C  153 LYS cc_start: 0.8604 (tmtt) cc_final: 0.8279 (tptp)
REVERT: C  226 LYS cc_start: 0.4600 (tptt) cc_final: 0.3365 (mtmm)
REVERT: C  312 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7753 (tm-30)
REVERT: C  343 ILE cc_start: 0.8736 (mp) cc_final: 0.8508 (mt)
REVERT: C  368 THR cc_start: 0.8236 (p) cc_final: 0.7926 (p)
REVERT: C  384 ASP cc_start: 0.7633 (m-30) cc_final: 0.7108 (t70)
REVERT: C  394 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: C  485 ASN cc_start: 0.8634 (t0) cc_final: 0.8311 (t0)
REVERT: D  153 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8374 (tptp)
REVERT: D  223 LEU cc_start: 0.8705 (tp) cc_final: 0.7625 (tp)
REVERT: D  224 VAL cc_start: 0.9359 (t) cc_final: 0.9124 (t)
REVERT: D  225 MET cc_start: 0.7939 (tpp) cc_final: 0.7705 (mpp)
REVERT: D  384 ASP cc_start: 0.7734 (m-30) cc_final: 0.7349 (t70)
REVERT: D  485 ASN cc_start: 0.8677 (t0) cc_final: 0.8363 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 346
  average time/residue: 0.1074
  time to fit residues: 54.4218
Evaluate side-chains
  284 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 127 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0050
   chunk 124 optimal weight:    9.9990
   chunk 97 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 147 HIS
C 281 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.177937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.146794 restraints weight = 25549.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.149873 restraints weight = 17091.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.152025 restraints weight = 12808.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.153531 restraints weight = 10355.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.154523 restraints weight = 8919.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.5249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  12716  Z= 0.162
  Angle     :  0.701   8.164  17136  Z= 0.368
  Chirality :  0.044   0.222   1916
  Planarity :  0.005   0.069   2160
  Dihedral  :  5.171  23.369   1624
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.22), residues: 1484
  helix:  0.95 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.45 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 167 
 TYR   0.019   0.002   TYR B 173 
 PHE   0.046   0.002   PHE B 464 
 TRP   0.088   0.004   TRP B 282 
 HIS   0.010   0.002   HIS C 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12716)
  covalent geometry    : angle       0.70090 (17136)
  hydrogen bonds       : bond        0.05723 (  900)
  hydrogen bonds       : angle       4.74330 ( 2676)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 351
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8303 (tptp)
REVERT: A  187 TYR cc_start: 0.8541 (m-80) cc_final: 0.7949 (m-80)
REVERT: A  223 LEU cc_start: 0.8705 (tp) cc_final: 0.7640 (tp)
REVERT: A  224 VAL cc_start: 0.9231 (t) cc_final: 0.8978 (t)
REVERT: A  356 HIS cc_start: 0.7071 (t-90) cc_final: 0.6562 (t70)
REVERT: A  368 THR cc_start: 0.8583 (p) cc_final: 0.8380 (p)
REVERT: A  384 ASP cc_start: 0.7544 (m-30) cc_final: 0.7025 (t70)
REVERT: A  399 MET cc_start: 0.8319 (tpp) cc_final: 0.7851 (tpp)
REVERT: B  153 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8351 (tptp)
REVERT: B  223 LEU cc_start: 0.8632 (tp) cc_final: 0.7850 (tp)
REVERT: B  399 MET cc_start: 0.8781 (tpp) cc_final: 0.8422 (tpp)
REVERT: C  153 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8266 (tptp)
REVERT: C  224 VAL cc_start: 0.9190 (t) cc_final: 0.8913 (t)
REVERT: C  312 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: C  343 ILE cc_start: 0.8823 (mp) cc_final: 0.8221 (mt)
REVERT: C  384 ASP cc_start: 0.7506 (m-30) cc_final: 0.7038 (t70)
REVERT: C  393 PHE cc_start: 0.8190 (m-80) cc_final: 0.7859 (m-80)
REVERT: C  394 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: C  485 ASN cc_start: 0.8709 (t0) cc_final: 0.8423 (t0)
REVERT: D  153 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8350 (tptp)
REVERT: D  223 LEU cc_start: 0.8652 (tp) cc_final: 0.7533 (tp)
REVERT: D  224 VAL cc_start: 0.9331 (t) cc_final: 0.9124 (t)
REVERT: D  225 MET cc_start: 0.8020 (tpp) cc_final: 0.7819 (mpp)
REVERT: D  226 LYS cc_start: 0.5023 (tptt) cc_final: 0.4748 (tptt)
REVERT: D  368 THR cc_start: 0.8334 (p) cc_final: 0.7968 (p)
REVERT: D  384 ASP cc_start: 0.7702 (m-30) cc_final: 0.7127 (t70)
REVERT: D  485 ASN cc_start: 0.8724 (t0) cc_final: 0.8358 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 351
  average time/residue: 0.1110
  time to fit residues: 56.7575
Evaluate side-chains
  285 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0870
   chunk 77 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 GLN
A 339 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.178934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.146434 restraints weight = 25203.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.149613 restraints weight = 16675.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.151824 restraints weight = 12421.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.153240 restraints weight = 10079.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.154341 restraints weight = 8773.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  12716  Z= 0.156
  Angle     :  0.684   8.194  17136  Z= 0.358
  Chirality :  0.044   0.200   1916
  Planarity :  0.004   0.039   2160
  Dihedral  :  5.067  22.212   1624
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.22), residues: 1484
  helix:  1.08 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.39 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 167 
 TYR   0.018   0.002   TYR B 173 
 PHE   0.041   0.002   PHE B 220 
 TRP   0.086   0.004   TRP B 282 
 HIS   0.009   0.001   HIS C 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12716)
  covalent geometry    : angle       0.68362 (17136)
  hydrogen bonds       : bond        0.05596 (  900)
  hydrogen bonds       : angle       4.68632 ( 2676)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2263.16 seconds
wall clock time: 40 minutes 5.08 seconds (2405.08 seconds total)