Starting phenix.real_space_refine
on Wed Jul 30 12:41:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6q0x_20555/07_2025/6q0x_20555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6q0x_20555/07_2025/6q0x_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6q0x_20555/07_2025/6q0x_20555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6q0x_20555/07_2025/6q0x_20555.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6q0x_20555/07_2025/6q0x_20555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6q0x_20555/07_2025/6q0x_20555.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.45, per 1000 atoms: 0.60
  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: 3.35
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.20
  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: 3.86

  Time building geometry restraints manager: 3.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             1.310
  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:          0.500
  Check model and map are aligned:         0.180
  Set scattering table:                    0.110
  Process input model:                     30.250
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.440
-------------------------------------------------------------------------------
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 : 24.04
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.83 (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
 TRP   0.019   0.002   TRP B 249 
 HIS   0.006   0.002   HIS D 306 
 PHE   0.025   0.002   PHE D 467 
 TYR   0.015   0.002   TYR B 297 
 ARG   0.004   0.001   ARG B 186 

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

*********************** 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  : 1.504 
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: 0.7341 (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: 0.7991 (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: 0.7974 (m-10) cc_final: 0.7757 (m-80)
REVERT: A  409 ARG cc_start: 0.7805 (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: 0.7658 (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: 0.7553 (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: 0.8645 (t)
REVERT: D  226 LYS cc_start: 0.4643 (tptm) cc_final: 0.4291 (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: 0.8429 (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: 0.8749 (mt) cc_final: 0.8248 (tt)
REVERT: D  393 PHE cc_start: 0.7970 (m-10) cc_final: 0.7762 (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: 0.2610
  time to fit residues: 158.6008
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  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.2980
   chunk 112 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   chunk 75 optimal weight:    0.4980
   chunk 59 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 281 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.176878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.144397 restraints weight = 25103.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.148002 restraints weight = 15492.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.150465 restraints weight = 11069.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  12716  Z= 0.189
  Angle     :  0.752   8.201  17136  Z= 0.393
  Chirality :  0.045   0.183   1916
  Planarity :  0.005   0.040   2160
  Dihedral  :  6.021  28.744   1624
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 19.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.21), residues: 1484
  helix: -0.38 (0.15), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.57 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 282 
 HIS   0.011   0.003   HIS C 154 
 PHE   0.027   0.003   PHE C 220 
 TYR   0.011   0.002   TYR D 173 
 ARG   0.006   0.001   ARG D 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06921 (  900)
  hydrogen bonds       : angle       5.28965 ( 2676)
  covalent geometry    : bond        0.00404 (12716)
  covalent geometry    : angle       0.75246 (17136)

*********************** 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
  392 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 384
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A  153 LYS cc_start: 0.8730 (tptp) cc_final: 0.8374 (tptp)
REVERT: A  260 GLU cc_start: 0.7331 (tp30) cc_final: 0.6495 (tm-30)
REVERT: A  270 PHE cc_start: 0.7659 (t80) cc_final: 0.7035 (m-80)
REVERT: A  312 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: A  337 VAL cc_start: 0.8780 (m) cc_final: 0.8493 (p)
REVERT: A  392 LEU cc_start: 0.8703 (mt) cc_final: 0.8174 (tt)
REVERT: A  399 MET cc_start: 0.8450 (tpp) cc_final: 0.8167 (tpp)
REVERT: A  485 ASN cc_start: 0.8672 (t0) cc_final: 0.8306 (t0)
REVERT: B  153 LYS cc_start: 0.8798 (tptp) cc_final: 0.8437 (tptp)
REVERT: B  270 PHE cc_start: 0.7752 (t80) cc_final: 0.7147 (m-80)
REVERT: B  281 GLN cc_start: 0.8915 (tm130) cc_final: 0.8696 (tm-30)
REVERT: B  312 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: B  337 VAL cc_start: 0.8787 (m) cc_final: 0.8493 (p)
REVERT: B  392 LEU cc_start: 0.8629 (mt) cc_final: 0.8044 (tt)
REVERT: B  394 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: B  399 MET cc_start: 0.8413 (tpp) cc_final: 0.8203 (tpp)
REVERT: C  153 LYS cc_start: 0.8731 (tptp) cc_final: 0.8358 (tptp)
REVERT: C  224 VAL cc_start: 0.9087 (t) cc_final: 0.8673 (t)
REVERT: C  227 HIS cc_start: 0.7344 (m170) cc_final: 0.6795 (m90)
REVERT: C  260 GLU cc_start: 0.7360 (tp30) cc_final: 0.6472 (tm-30)
REVERT: C  270 PHE cc_start: 0.7653 (t80) cc_final: 0.7055 (m-80)
REVERT: C  312 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: C  337 VAL cc_start: 0.8789 (m) cc_final: 0.8478 (p)
REVERT: C  392 LEU cc_start: 0.8648 (mt) cc_final: 0.8128 (tt)
REVERT: C  394 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7865 (mt-10)
REVERT: C  399 MET cc_start: 0.8504 (tpp) cc_final: 0.8294 (tpp)
REVERT: C  485 ASN cc_start: 0.8665 (t0) cc_final: 0.8257 (t0)
REVERT: D  153 LYS cc_start: 0.8757 (tptp) cc_final: 0.8388 (tptp)
REVERT: D  224 VAL cc_start: 0.9034 (t) cc_final: 0.8580 (t)
REVERT: D  260 GLU cc_start: 0.7341 (tp30) cc_final: 0.6523 (tm-30)
REVERT: D  270 PHE cc_start: 0.7805 (t80) cc_final: 0.7147 (m-80)
REVERT: D  309 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7910 (ttm-80)
REVERT: D  312 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: D  337 VAL cc_start: 0.8818 (m) cc_final: 0.8540 (p)
REVERT: D  392 LEU cc_start: 0.8702 (mt) cc_final: 0.8154 (tt)
REVERT: D  394 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7799 (mt-10)
REVERT: D  399 MET cc_start: 0.8508 (tpp) cc_final: 0.8187 (tpp)
REVERT: D  485 ASN cc_start: 0.8647 (t0) cc_final: 0.8211 (t0)
  outliers start: 8
  outliers final: 0
  residues processed: 388
  average time/residue: 0.2480
  time to fit residues: 136.3854
Evaluate side-chains
  307 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 128 optimal weight:    4.9990
   chunk 123 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 119 optimal weight:    9.9990
   chunk 111 optimal weight:    7.9990
   chunk 95 optimal weight:    7.9990
   chunk 145 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 127 optimal weight:    3.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 356 HIS ** 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 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 449 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.171548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.138957 restraints weight = 25561.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.142273 restraints weight = 16280.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.144559 restraints weight = 11844.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  12716  Z= 0.231
  Angle     :  0.738   7.675  17136  Z= 0.399
  Chirality :  0.043   0.150   1916
  Planarity :  0.005   0.039   2160
  Dihedral  :  5.887  27.913   1624
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  6.43 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.22), residues: 1484
  helix:  0.16 (0.15), residues: 1072
  sheet:  None (None), residues: 0
  loop : -2.46 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 282 
 HIS   0.011   0.002   HIS D 227 
 PHE   0.035   0.003   PHE A 220 
 TYR   0.015   0.002   TYR D 150 
 ARG   0.008   0.001   ARG C 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06654 (  900)
  hydrogen bonds       : angle       5.22827 ( 2676)
  covalent geometry    : bond        0.00514 (12716)
  covalent geometry    : angle       0.73813 (17136)

*********************** 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
  349 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 338
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8784 (tptp) cc_final: 0.8493 (tptp)
REVERT: A  181 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8581 (mm-30)
REVERT: A  213 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7584 (tpp80)
REVERT: A  224 VAL cc_start: 0.9170 (t) cc_final: 0.8874 (t)
REVERT: A  244 THR cc_start: 0.7721 (t) cc_final: 0.7188 (t)
REVERT: A  394 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7766 (mt-10)
REVERT: A  399 MET cc_start: 0.8603 (tpp) cc_final: 0.8021 (tpp)
REVERT: A  485 ASN cc_start: 0.8793 (t0) cc_final: 0.8477 (t0)
REVERT: B  181 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8548 (mm-30)
REVERT: B  213 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7664 (tpp80)
REVERT: B  244 THR cc_start: 0.7711 (t) cc_final: 0.7172 (t)
REVERT: B  281 GLN cc_start: 0.8912 (pp30) cc_final: 0.8349 (pp30)
REVERT: B  293 MET cc_start: 0.8879 (tpp) cc_final: 0.8382 (tmm)
REVERT: B  394 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7917 (mt-10)
REVERT: B  399 MET cc_start: 0.8521 (tpp) cc_final: 0.8244 (tpp)
REVERT: C  153 LYS cc_start: 0.8812 (tptp) cc_final: 0.8494 (tptp)
REVERT: C  213 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7563 (tpp80)
REVERT: C  224 VAL cc_start: 0.9116 (t) cc_final: 0.8749 (t)
REVERT: C  227 HIS cc_start: 0.7345 (m170) cc_final: 0.6837 (m90)
REVERT: C  244 THR cc_start: 0.7681 (t) cc_final: 0.7181 (t)
REVERT: C  260 GLU cc_start: 0.7517 (tp30) cc_final: 0.6692 (tm-30)
REVERT: C  270 PHE cc_start: 0.7800 (t80) cc_final: 0.7070 (m-80)
REVERT: C  357 LEU cc_start: 0.9265 (mt) cc_final: 0.8889 (mt)
REVERT: C  392 LEU cc_start: 0.8818 (mt) cc_final: 0.8192 (tt)
REVERT: C  399 MET cc_start: 0.8533 (tpp) cc_final: 0.8124 (tpp)
REVERT: C  485 ASN cc_start: 0.8765 (t0) cc_final: 0.8423 (t0)
REVERT: D  213 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7599 (tpp80)
REVERT: D  224 VAL cc_start: 0.9192 (t) cc_final: 0.8878 (t)
REVERT: D  244 THR cc_start: 0.7723 (t) cc_final: 0.7192 (t)
REVERT: D  485 ASN cc_start: 0.8788 (t0) cc_final: 0.8423 (t0)
  outliers start: 11
  outliers final: 0
  residues processed: 345
  average time/residue: 0.2623
  time to fit residues: 126.7986
Evaluate side-chains
  263 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 118 optimal weight:    4.9990
   chunk 95 optimal weight:    0.2980
   chunk 103 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9980
   overall best weight:    2.4586

-------------------------------------------------------------------------------
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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 ASN
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
C 449 GLN
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 449 GLN
** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.171009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.138929 restraints weight = 25837.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.142142 restraints weight = 16671.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.144344 restraints weight = 12222.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12716  Z= 0.206
  Angle     :  0.704   7.735  17136  Z= 0.377
  Chirality :  0.043   0.148   1916
  Planarity :  0.005   0.046   2160
  Dihedral  :  5.795  27.256   1624
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  4.29 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.22), residues: 1484
  helix:  0.45 (0.16), residues: 1048
  sheet:  None (None), residues: 0
  loop : -2.30 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP B 282 
 HIS   0.012   0.002   HIS A 227 
 PHE   0.040   0.002   PHE B 220 
 TYR   0.012   0.002   TYR B 187 
 ARG   0.005   0.001   ARG D 309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06441 (  900)
  hydrogen bonds       : angle       5.06340 ( 2676)
  covalent geometry    : bond        0.00448 (12716)
  covalent geometry    : angle       0.70380 (17136)

*********************** 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
  357 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 350
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8801 (tptp) cc_final: 0.8434 (tptp)
REVERT: A  213 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7592 (tpp80)
REVERT: A  224 VAL cc_start: 0.9183 (t) cc_final: 0.8870 (t)
REVERT: A  357 LEU cc_start: 0.9270 (mt) cc_final: 0.8860 (mt)
REVERT: A  384 ASP cc_start: 0.8181 (m-30) cc_final: 0.7621 (t70)
REVERT: A  399 MET cc_start: 0.8557 (tpp) cc_final: 0.7982 (tpp)
REVERT: A  485 ASN cc_start: 0.8826 (t0) cc_final: 0.8593 (t0)
REVERT: B  153 LYS cc_start: 0.8742 (tmtt) cc_final: 0.8412 (tptp)
REVERT: B  172 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7730 (mtm110)
REVERT: B  224 VAL cc_start: 0.9225 (t) cc_final: 0.8944 (t)
REVERT: B  293 MET cc_start: 0.8859 (tpp) cc_final: 0.8399 (tmm)
REVERT: B  311 MET cc_start: 0.7478 (tpt) cc_final: 0.7270 (tpt)
REVERT: B  384 ASP cc_start: 0.8260 (m-30) cc_final: 0.7651 (t70)
REVERT: B  394 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7828 (mt-10)
REVERT: B  399 MET cc_start: 0.8503 (tpp) cc_final: 0.7969 (tpp)
REVERT: C  153 LYS cc_start: 0.8847 (tptp) cc_final: 0.8629 (tmtt)
REVERT: C  224 VAL cc_start: 0.9151 (t) cc_final: 0.8734 (t)
REVERT: C  227 HIS cc_start: 0.7234 (m170) cc_final: 0.6853 (m90)
REVERT: C  282 TRP cc_start: 0.8476 (p90) cc_final: 0.8168 (p90)
REVERT: C  312 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: C  357 LEU cc_start: 0.9274 (mt) cc_final: 0.8864 (mt)
REVERT: C  399 MET cc_start: 0.8594 (tpp) cc_final: 0.8244 (tpp)
REVERT: C  485 ASN cc_start: 0.8791 (t0) cc_final: 0.8469 (t0)
REVERT: D  153 LYS cc_start: 0.8819 (tptp) cc_final: 0.8607 (tmtt)
REVERT: D  181 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8580 (mm-30)
REVERT: D  224 VAL cc_start: 0.9189 (t) cc_final: 0.8923 (t)
REVERT: D  484 LEU cc_start: 0.8518 (mt) cc_final: 0.8308 (mt)
REVERT: D  485 ASN cc_start: 0.8852 (t0) cc_final: 0.8575 (t0)
  outliers start: 7
  outliers final: 0
  residues processed: 354
  average time/residue: 0.2700
  time to fit residues: 131.7509
Evaluate side-chains
  283 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 139 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 71 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 112 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 103 optimal weight:    0.2980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 ASN
C 281 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.173285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.141301 restraints weight = 25653.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.144506 restraints weight = 16565.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.146819 restraints weight = 12200.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12716  Z= 0.182
  Angle     :  0.682   7.188  17136  Z= 0.362
  Chirality :  0.043   0.209   1916
  Planarity :  0.004   0.040   2160
  Dihedral  :  5.639  26.995   1624
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.00 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.22), residues: 1484
  helix:  0.55 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.37 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.003   TRP D 282 
 HIS   0.011   0.002   HIS D 227 
 PHE   0.039   0.003   PHE C 220 
 TYR   0.013   0.001   TYR C 173 
 ARG   0.007   0.001   ARG D 443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06403 (  900)
  hydrogen bonds       : angle       4.95402 ( 2676)
  covalent geometry    : bond        0.00400 (12716)
  covalent geometry    : angle       0.68189 (17136)

*********************** 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
  339 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 336
  time to evaluate  : 1.417 
Fit side-chains
REVERT: A  153 LYS cc_start: 0.8753 (tptp) cc_final: 0.8355 (tptp)
REVERT: A  224 VAL cc_start: 0.9182 (t) cc_final: 0.8976 (t)
REVERT: A  312 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: A  357 LEU cc_start: 0.9210 (mt) cc_final: 0.8857 (mt)
REVERT: A  384 ASP cc_start: 0.8095 (m-30) cc_final: 0.7583 (t70)
REVERT: A  399 MET cc_start: 0.8477 (tpp) cc_final: 0.7879 (tpp)
REVERT: A  485 ASN cc_start: 0.8837 (t0) cc_final: 0.8585 (t0)
REVERT: B  153 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8402 (tptp)
REVERT: B  224 VAL cc_start: 0.9227 (t) cc_final: 0.8914 (t)
REVERT: B  281 GLN cc_start: 0.8971 (pp30) cc_final: 0.8750 (pp30)
REVERT: B  293 MET cc_start: 0.8871 (tpp) cc_final: 0.8531 (tmm)
REVERT: B  307 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7345 (tp30)
REVERT: B  311 MET cc_start: 0.7430 (tpt) cc_final: 0.6832 (tpt)
REVERT: B  357 LEU cc_start: 0.9267 (mt) cc_final: 0.8944 (mt)
REVERT: B  384 ASP cc_start: 0.8205 (m-30) cc_final: 0.7659 (t70)
REVERT: B  399 MET cc_start: 0.8475 (tpp) cc_final: 0.8269 (tpp)
REVERT: B  421 MET cc_start: 0.6147 (tpt) cc_final: 0.5743 (ppp)
REVERT: C  153 LYS cc_start: 0.8781 (tptp) cc_final: 0.8434 (tptp)
REVERT: C  224 VAL cc_start: 0.9205 (t) cc_final: 0.8730 (t)
REVERT: C  227 HIS cc_start: 0.7140 (m170) cc_final: 0.6809 (m90)
REVERT: C  294 GLU cc_start: 0.8323 (tt0) cc_final: 0.7917 (tt0)
REVERT: C  312 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: C  357 LEU cc_start: 0.9177 (mt) cc_final: 0.8842 (mt)
REVERT: C  384 ASP cc_start: 0.8210 (m-30) cc_final: 0.7645 (t70)
REVERT: C  399 MET cc_start: 0.8469 (tpp) cc_final: 0.8099 (tpp)
REVERT: C  485 ASN cc_start: 0.8743 (t0) cc_final: 0.8408 (t0)
REVERT: D  153 LYS cc_start: 0.8806 (tptp) cc_final: 0.8409 (tptp)
REVERT: D  224 VAL cc_start: 0.9181 (t) cc_final: 0.8933 (t)
REVERT: D  343 ILE cc_start: 0.8913 (mp) cc_final: 0.8654 (mt)
REVERT: D  357 LEU cc_start: 0.9180 (mt) cc_final: 0.8868 (mt)
REVERT: D  384 ASP cc_start: 0.8141 (m-30) cc_final: 0.7609 (t70)
REVERT: D  485 ASN cc_start: 0.8813 (t0) cc_final: 0.8515 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 336
  average time/residue: 0.2362
  time to fit residues: 114.0406
Evaluate side-chains
  273 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 132 optimal weight:   10.0000
   chunk 65 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0370
   chunk 99 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 121 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.9262

-------------------------------------------------------------------------------
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 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
C 449 GLN
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 GLN
D 449 GLN
** 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 = 0.4268 r_free = 0.4268 target = 0.172363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.142047 restraints weight = 25578.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.144951 restraints weight = 17074.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.146953 restraints weight = 12809.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12716  Z= 0.182
  Angle     :  0.678   6.617  17136  Z= 0.360
  Chirality :  0.043   0.154   1916
  Planarity :  0.004   0.042   2160
  Dihedral  :  5.551  26.117   1624
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.43 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.22), residues: 1484
  helix:  0.69 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.36 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.003   TRP D 282 
 HIS   0.010   0.002   HIS D 227 
 PHE   0.044   0.003   PHE C 220 
 TYR   0.009   0.001   TYR A 150 
 ARG   0.004   0.001   ARG D 309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06185 (  900)
  hydrogen bonds       : angle       4.89582 ( 2676)
  covalent geometry    : bond        0.00396 (12716)
  covalent geometry    : angle       0.67816 (17136)

*********************** 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
  341 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 338
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8659 (tptp) cc_final: 0.8351 (tptp)
REVERT: A  223 LEU cc_start: 0.8702 (tp) cc_final: 0.7979 (tp)
REVERT: A  312 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: A  357 LEU cc_start: 0.9230 (mt) cc_final: 0.8866 (mt)
REVERT: A  368 THR cc_start: 0.8537 (p) cc_final: 0.8290 (p)
REVERT: A  384 ASP cc_start: 0.8081 (m-30) cc_final: 0.7552 (t70)
REVERT: A  399 MET cc_start: 0.8446 (tpp) cc_final: 0.7952 (tpp)
REVERT: A  421 MET cc_start: 0.6311 (tpt) cc_final: 0.5911 (ppp)
REVERT: A  485 ASN cc_start: 0.8765 (t0) cc_final: 0.8537 (t0)
REVERT: B  153 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8444 (tptp)
REVERT: B  223 LEU cc_start: 0.8735 (tp) cc_final: 0.7875 (tp)
REVERT: B  224 VAL cc_start: 0.9268 (t) cc_final: 0.9002 (t)
REVERT: B  293 MET cc_start: 0.8782 (tpp) cc_final: 0.8562 (tmm)
REVERT: B  307 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7269 (tp30)
REVERT: B  311 MET cc_start: 0.7301 (tpt) cc_final: 0.6633 (tpt)
REVERT: B  357 LEU cc_start: 0.9241 (mt) cc_final: 0.8925 (mt)
REVERT: B  368 THR cc_start: 0.8583 (p) cc_final: 0.8378 (p)
REVERT: B  384 ASP cc_start: 0.8158 (m-30) cc_final: 0.7614 (t70)
REVERT: B  399 MET cc_start: 0.8497 (tpp) cc_final: 0.8284 (tpp)
REVERT: B  421 MET cc_start: 0.6095 (tpt) cc_final: 0.5727 (ppp)
REVERT: C  153 LYS cc_start: 0.8736 (tptp) cc_final: 0.8404 (tptp)
REVERT: C  224 VAL cc_start: 0.9241 (t) cc_final: 0.8749 (t)
REVERT: C  227 HIS cc_start: 0.6974 (m170) cc_final: 0.6700 (m90)
REVERT: C  312 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7628 (tm-30)
REVERT: C  357 LEU cc_start: 0.9208 (mt) cc_final: 0.8855 (mt)
REVERT: C  384 ASP cc_start: 0.8169 (m-30) cc_final: 0.7588 (t70)
REVERT: C  399 MET cc_start: 0.8512 (tpp) cc_final: 0.8165 (tpp)
REVERT: C  421 MET cc_start: 0.6354 (tpt) cc_final: 0.5912 (ppp)
REVERT: C  485 ASN cc_start: 0.8671 (t0) cc_final: 0.8389 (t0)
REVERT: D  153 LYS cc_start: 0.8721 (tptp) cc_final: 0.8383 (tptp)
REVERT: D  224 VAL cc_start: 0.9252 (t) cc_final: 0.9012 (t)
REVERT: D  311 MET cc_start: 0.7512 (tpt) cc_final: 0.6938 (tpt)
REVERT: D  357 LEU cc_start: 0.9251 (mt) cc_final: 0.8889 (mt)
REVERT: D  368 THR cc_start: 0.8582 (p) cc_final: 0.8330 (p)
REVERT: D  384 ASP cc_start: 0.8146 (m-30) cc_final: 0.7587 (t70)
REVERT: D  421 MET cc_start: 0.6280 (tpt) cc_final: 0.5914 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 338
  average time/residue: 0.2571
  time to fit residues: 122.9006
Evaluate side-chains
  263 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 103 optimal weight:    0.0370
   chunk 147 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 116 optimal weight:    0.6980
   overall best weight:    1.3464

-------------------------------------------------------------------------------
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 449 GLN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS
** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
C 449 GLN
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 147 HIS
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 449 GLN
** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 485 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.172574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.142800 restraints weight = 25114.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.146158 restraints weight = 15862.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.148426 restraints weight = 11382.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12716  Z= 0.175
  Angle     :  0.683   7.155  17136  Z= 0.362
  Chirality :  0.043   0.198   1916
  Planarity :  0.005   0.084   2160
  Dihedral  :  5.533  24.644   1624
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.64 %
    Favored  : 97.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.22), residues: 1484
  helix:  0.78 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.42 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.003   TRP B 282 
 HIS   0.009   0.002   HIS B 227 
 PHE   0.043   0.002   PHE A 220 
 TYR   0.017   0.002   TYR A 187 
 ARG   0.014   0.001   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06090 (  900)
  hydrogen bonds       : angle       4.86128 ( 2676)
  covalent geometry    : bond        0.00371 (12716)
  covalent geometry    : angle       0.68314 (17136)

*********************** 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
  341 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 338
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8781 (tptm) cc_final: 0.8394 (tptp)
REVERT: A  223 LEU cc_start: 0.8686 (tp) cc_final: 0.7890 (tp)
REVERT: A  224 VAL cc_start: 0.9257 (t) cc_final: 0.9017 (t)
REVERT: A  226 LYS cc_start: 0.4778 (tptt) cc_final: 0.4301 (tptm)
REVERT: A  307 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7374 (tp30)
REVERT: A  312 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7782 (tm-30)
REVERT: A  357 LEU cc_start: 0.9267 (mt) cc_final: 0.8887 (mt)
REVERT: A  368 THR cc_start: 0.8662 (p) cc_final: 0.8427 (p)
REVERT: A  384 ASP cc_start: 0.8054 (m-30) cc_final: 0.7425 (t70)
REVERT: A  399 MET cc_start: 0.8482 (tpp) cc_final: 0.7963 (tpp)
REVERT: A  421 MET cc_start: 0.6427 (tpt) cc_final: 0.5974 (ppp)
REVERT: A  485 ASN cc_start: 0.8901 (t0) cc_final: 0.8560 (t0)
REVERT: B  153 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8432 (tptp)
REVERT: B  223 LEU cc_start: 0.8604 (tp) cc_final: 0.7833 (tp)
REVERT: B  224 VAL cc_start: 0.9157 (t) cc_final: 0.8891 (t)
REVERT: B  226 LYS cc_start: 0.5140 (tptt) cc_final: 0.3695 (mtmm)
REVERT: B  307 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7255 (tp30)
REVERT: B  311 MET cc_start: 0.7341 (tpt) cc_final: 0.6657 (tpt)
REVERT: B  357 LEU cc_start: 0.9273 (mt) cc_final: 0.8900 (mt)
REVERT: B  368 THR cc_start: 0.8687 (p) cc_final: 0.8467 (p)
REVERT: B  384 ASP cc_start: 0.8202 (m-30) cc_final: 0.7469 (t70)
REVERT: B  399 MET cc_start: 0.8521 (tpp) cc_final: 0.8269 (tpp)
REVERT: B  421 MET cc_start: 0.5986 (tpt) cc_final: 0.5692 (ppp)
REVERT: C  153 LYS cc_start: 0.8808 (tptm) cc_final: 0.8429 (tptp)
REVERT: C  224 VAL cc_start: 0.9177 (t) cc_final: 0.8758 (t)
REVERT: C  227 HIS cc_start: 0.6994 (m170) cc_final: 0.6723 (m90)
REVERT: C  312 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: C  329 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7533 (mp0)
REVERT: C  357 LEU cc_start: 0.9213 (mt) cc_final: 0.8923 (mm)
REVERT: C  384 ASP cc_start: 0.8152 (m-30) cc_final: 0.7487 (t70)
REVERT: C  399 MET cc_start: 0.8509 (tpp) cc_final: 0.8198 (tpp)
REVERT: C  421 MET cc_start: 0.6380 (tpt) cc_final: 0.5955 (ppp)
REVERT: C  485 ASN cc_start: 0.8752 (t0) cc_final: 0.8405 (t0)
REVERT: D  153 LYS cc_start: 0.8775 (tptm) cc_final: 0.8397 (tptp)
REVERT: D  224 VAL cc_start: 0.9141 (t) cc_final: 0.8934 (t)
REVERT: D  281 GLN cc_start: 0.8854 (pp30) cc_final: 0.8614 (pp30)
REVERT: D  311 MET cc_start: 0.7343 (tpt) cc_final: 0.6804 (tpt)
REVERT: D  357 LEU cc_start: 0.9258 (mt) cc_final: 0.8878 (mt)
REVERT: D  384 ASP cc_start: 0.8139 (m-30) cc_final: 0.7473 (t70)
REVERT: D  421 MET cc_start: 0.6160 (tpt) cc_final: 0.5867 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 338
  average time/residue: 0.2255
  time to fit residues: 110.9200
Evaluate side-chains
  275 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 141 optimal weight:    6.9990
   chunk 133 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 147 HIS
C 281 GLN
C 449 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 449 GLN
** 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 = 0.4296 r_free = 0.4296 target = 0.174430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.143717 restraints weight = 25378.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.147179 restraints weight = 15948.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.149474 restraints weight = 11404.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.4640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12716  Z= 0.165
  Angle     :  0.678   6.883  17136  Z= 0.362
  Chirality :  0.044   0.176   1916
  Planarity :  0.005   0.053   2160
  Dihedral  :  5.424  24.552   1624
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 17.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.93 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.22), residues: 1484
  helix:  0.89 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.43 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.003   TRP D 282 
 HIS   0.009   0.001   HIS D 356 
 PHE   0.043   0.002   PHE C 220 
 TYR   0.015   0.002   TYR D 173 
 ARG   0.012   0.001   ARG D 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05972 (  900)
  hydrogen bonds       : angle       4.82408 ( 2676)
  covalent geometry    : bond        0.00352 (12716)
  covalent geometry    : angle       0.67796 (17136)

*********************** 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
  356 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 353
  time to evaluate  : 2.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8616 (m-80) cc_final: 0.8165 (m-80)
REVERT: A  223 LEU cc_start: 0.8747 (tp) cc_final: 0.7947 (tp)
REVERT: A  226 LYS cc_start: 0.4903 (tptt) cc_final: 0.4551 (tptm)
REVERT: A  312 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A  357 LEU cc_start: 0.9236 (mt) cc_final: 0.8842 (mt)
REVERT: A  368 THR cc_start: 0.8500 (p) cc_final: 0.8245 (p)
REVERT: A  384 ASP cc_start: 0.7905 (m-30) cc_final: 0.7321 (t70)
REVERT: A  394 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8108 (mt-10)
REVERT: A  399 MET cc_start: 0.8391 (tpp) cc_final: 0.7887 (tpp)
REVERT: A  421 MET cc_start: 0.6282 (tpt) cc_final: 0.5942 (ppp)
REVERT: A  485 ASN cc_start: 0.8810 (t0) cc_final: 0.8555 (t0)
REVERT: B  153 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8423 (tptp)
REVERT: B  223 LEU cc_start: 0.8684 (tp) cc_final: 0.7956 (tp)
REVERT: B  224 VAL cc_start: 0.9232 (t) cc_final: 0.9002 (t)
REVERT: B  226 LYS cc_start: 0.5199 (tptt) cc_final: 0.4721 (tptm)
REVERT: B  311 MET cc_start: 0.7157 (tpt) cc_final: 0.6705 (tpt)
REVERT: B  312 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: B  357 LEU cc_start: 0.9260 (mt) cc_final: 0.8868 (mt)
REVERT: B  368 THR cc_start: 0.8527 (p) cc_final: 0.7960 (p)
REVERT: B  384 ASP cc_start: 0.8012 (m-30) cc_final: 0.7384 (t70)
REVERT: B  399 MET cc_start: 0.8462 (tpp) cc_final: 0.8233 (tpp)
REVERT: B  421 MET cc_start: 0.5945 (tpt) cc_final: 0.5741 (ppp)
REVERT: C  224 VAL cc_start: 0.9236 (t) cc_final: 0.8808 (t)
REVERT: C  227 HIS cc_start: 0.6934 (m170) cc_final: 0.6706 (m90)
REVERT: C  311 MET cc_start: 0.7394 (tpt) cc_final: 0.7047 (tpt)
REVERT: C  312 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: C  357 LEU cc_start: 0.9182 (mt) cc_final: 0.8815 (mt)
REVERT: C  384 ASP cc_start: 0.8072 (m-30) cc_final: 0.7457 (t70)
REVERT: C  399 MET cc_start: 0.8455 (tpp) cc_final: 0.8119 (tpp)
REVERT: C  421 MET cc_start: 0.6163 (tpt) cc_final: 0.5846 (ppp)
REVERT: C  485 ASN cc_start: 0.8679 (t0) cc_final: 0.8418 (t0)
REVERT: D  153 LYS cc_start: 0.8686 (tptm) cc_final: 0.8401 (tptp)
REVERT: D  223 LEU cc_start: 0.8603 (tp) cc_final: 0.7837 (tp)
REVERT: D  224 VAL cc_start: 0.9181 (t) cc_final: 0.8969 (t)
REVERT: D  307 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7225 (tp30)
REVERT: D  312 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8000 (tm-30)
REVERT: D  368 THR cc_start: 0.8519 (p) cc_final: 0.8292 (p)
REVERT: D  384 ASP cc_start: 0.8028 (m-30) cc_final: 0.7413 (t70)
REVERT: D  421 MET cc_start: 0.6098 (tpt) cc_final: 0.5845 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 353
  average time/residue: 0.2754
  time to fit residues: 139.1162
Evaluate side-chains
  281 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 137 optimal weight:    0.9980
   chunk 49 optimal weight:    0.1980
   chunk 45 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 125 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 145 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0670
   chunk 122 optimal weight:    0.3980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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
** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.178058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.148115 restraints weight = 25412.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.151483 restraints weight = 16201.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.153888 restraints weight = 11564.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12716  Z= 0.156
  Angle     :  0.671   7.733  17136  Z= 0.355
  Chirality :  0.043   0.242   1916
  Planarity :  0.004   0.038   2160
  Dihedral  :  5.276  24.022   1624
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.22), residues: 1484
  helix:  1.03 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.45 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.086   0.003   TRP D 282 
 HIS   0.010   0.001   HIS D 227 
 PHE   0.039   0.002   PHE A 220 
 TYR   0.018   0.001   TYR D 173 
 ARG   0.009   0.001   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05811 (  900)
  hydrogen bonds       : angle       4.69442 ( 2676)
  covalent geometry    : bond        0.00331 (12716)
  covalent geometry    : angle       0.67055 (17136)

*********************** 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
  356 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 356
  time to evaluate  : 1.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.8573 (m-80) cc_final: 0.8127 (m-80)
REVERT: A  211 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8579 (ptmm)
REVERT: A  223 LEU cc_start: 0.8700 (tp) cc_final: 0.7908 (tp)
REVERT: A  224 VAL cc_start: 0.9329 (t) cc_final: 0.9108 (t)
REVERT: A  226 LYS cc_start: 0.4979 (tptt) cc_final: 0.4559 (tptt)
REVERT: A  312 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: A  357 LEU cc_start: 0.9241 (mt) cc_final: 0.8835 (mt)
REVERT: A  368 THR cc_start: 0.8523 (p) cc_final: 0.8284 (p)
REVERT: A  384 ASP cc_start: 0.7683 (m-30) cc_final: 0.7127 (t70)
REVERT: A  394 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8110 (mt-10)
REVERT: A  399 MET cc_start: 0.8325 (tpp) cc_final: 0.7787 (tpp)
REVERT: B  153 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8420 (tptp)
REVERT: B  223 LEU cc_start: 0.8607 (tp) cc_final: 0.7929 (tp)
REVERT: B  224 VAL cc_start: 0.9155 (t) cc_final: 0.8919 (t)
REVERT: B  311 MET cc_start: 0.7034 (tpt) cc_final: 0.6697 (tpt)
REVERT: B  384 ASP cc_start: 0.7859 (m-30) cc_final: 0.7244 (t70)
REVERT: C  211 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8561 (ptmm)
REVERT: C  224 VAL cc_start: 0.9079 (t) cc_final: 0.8695 (t)
REVERT: C  311 MET cc_start: 0.7260 (tpt) cc_final: 0.6864 (tpt)
REVERT: C  312 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: C  384 ASP cc_start: 0.7798 (m-30) cc_final: 0.7158 (t70)
REVERT: C  393 PHE cc_start: 0.8063 (m-10) cc_final: 0.7846 (m-80)
REVERT: C  399 MET cc_start: 0.8347 (tpp) cc_final: 0.8097 (tpp)
REVERT: C  485 ASN cc_start: 0.8732 (t0) cc_final: 0.8411 (t0)
REVERT: D  153 LYS cc_start: 0.8840 (tptm) cc_final: 0.8524 (tptp)
REVERT: D  226 LYS cc_start: 0.4683 (tptt) cc_final: 0.4328 (tptm)
REVERT: D  311 MET cc_start: 0.7223 (tpt) cc_final: 0.6583 (tpt)
REVERT: D  312 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: D  368 THR cc_start: 0.8512 (p) cc_final: 0.8226 (p)
REVERT: D  384 ASP cc_start: 0.7870 (m-30) cc_final: 0.7320 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 356
  average time/residue: 0.2715
  time to fit residues: 139.3532
Evaluate side-chains
  294 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 147 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0970
   chunk 45 optimal weight:    8.9990
   chunk 115 optimal weight:    2.9990
   chunk 125 optimal weight:   10.0000
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 GLN
** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.178135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.147444 restraints weight = 25062.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.150798 restraints weight = 16246.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.152852 restraints weight = 11811.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
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      :  0.003   0.065  12716  Z= 0.160
  Angle     :  0.704   9.001  17136  Z= 0.369
  Chirality :  0.044   0.200   1916
  Planarity :  0.004   0.036   2160
  Dihedral  :  5.260  23.228   1624
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.64 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.22), residues: 1484
  helix:  1.01 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.55 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.090   0.004   TRP D 282 
 HIS   0.019   0.002   HIS C 227 
 PHE   0.041   0.002   PHE A 220 
 TYR   0.017   0.001   TYR D 173 
 ARG   0.008   0.001   ARG D 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05760 (  900)
  hydrogen bonds       : angle       4.72861 ( 2676)
  covalent geometry    : bond        0.00342 (12716)
  covalent geometry    : angle       0.70371 (17136)

********************** 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
  356 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 355
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 LYS cc_start: 0.8795 (tptm) cc_final: 0.8421 (tptp)
REVERT: A  177 LEU cc_start: 0.8217 (mm) cc_final: 0.7997 (mm)
REVERT: A  187 TYR cc_start: 0.8584 (m-80) cc_final: 0.8107 (m-80)
REVERT: A  223 LEU cc_start: 0.8564 (tp) cc_final: 0.7414 (tp)
REVERT: A  312 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  384 ASP cc_start: 0.7666 (m-30) cc_final: 0.7008 (t70)
REVERT: A  394 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8126 (mt-10)
REVERT: A  399 MET cc_start: 0.8287 (tpp) cc_final: 0.7828 (tpp)
REVERT: A  485 ASN cc_start: 0.8838 (t0) cc_final: 0.8438 (t0)
REVERT: B  153 LYS cc_start: 0.8742 (tmtt) cc_final: 0.8461 (tmtt)
REVERT: B  223 LEU cc_start: 0.8664 (tp) cc_final: 0.8020 (tp)
REVERT: B  226 LYS cc_start: 0.4687 (tptt) cc_final: 0.3709 (tmtt)
REVERT: B  311 MET cc_start: 0.7095 (tpt) cc_final: 0.6734 (tpt)
REVERT: B  358 GLU cc_start: 0.8713 (tp30) cc_final: 0.8120 (tp30)
REVERT: B  368 THR cc_start: 0.8393 (p) cc_final: 0.8113 (p)
REVERT: B  384 ASP cc_start: 0.7871 (m-30) cc_final: 0.7236 (t70)
REVERT: C  153 LYS cc_start: 0.8875 (tptm) cc_final: 0.8556 (tptp)
REVERT: C  224 VAL cc_start: 0.9045 (t) cc_final: 0.8669 (t)
REVERT: C  311 MET cc_start: 0.7284 (tpt) cc_final: 0.6915 (tpt)
REVERT: C  312 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7844 (tm-30)
REVERT: C  384 ASP cc_start: 0.7691 (m-30) cc_final: 0.7201 (t70)
REVERT: C  499 LEU cc_start: 0.8869 (tp) cc_final: 0.8639 (tp)
REVERT: D  153 LYS cc_start: 0.8829 (tptm) cc_final: 0.8502 (tptp)
REVERT: D  177 LEU cc_start: 0.8169 (mm) cc_final: 0.7906 (mm)
REVERT: D  223 LEU cc_start: 0.8577 (tp) cc_final: 0.7925 (tp)
REVERT: D  311 MET cc_start: 0.7024 (tpt) cc_final: 0.6612 (tpt)
REVERT: D  312 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: D  384 ASP cc_start: 0.7822 (m-30) cc_final: 0.7211 (t70)
REVERT: D  392 LEU cc_start: 0.8236 (mt) cc_final: 0.7985 (tt)
REVERT: D  485 ASN cc_start: 0.9073 (t0) cc_final: 0.8854 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 356
  average time/residue: 0.2317
  time to fit residues: 119.6887
Evaluate side-chains
  291 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 134 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 147 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 144 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 GLN
** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.174549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.144137 restraints weight = 25089.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.147351 restraints weight = 16132.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.149549 restraints weight = 11746.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.5279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  12716  Z= 0.181
  Angle     :  0.721  10.517  17136  Z= 0.379
  Chirality :  0.044   0.194   1916
  Planarity :  0.005   0.040   2160
  Dihedral  :  5.276  23.266   1624
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.22), residues: 1484
  helix:  1.00 (0.16), residues: 1068
  sheet:  None (None), residues: 0
  loop : -2.58 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.088   0.004   TRP B 282 
 HIS   0.014   0.002   HIS C 227 
 PHE   0.044   0.003   PHE A 220 
 TYR   0.015   0.002   TYR D 173 
 ARG   0.009   0.001   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05710 (  900)
  hydrogen bonds       : angle       4.83920 ( 2676)
  covalent geometry    : bond        0.00417 (12716)
  covalent geometry    : angle       0.72103 (17136)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4320.39 seconds
wall clock time: 76 minutes 40.20 seconds (4600.20 seconds total)