Starting phenix.real_space_refine
on Sun Jun 15 22:01:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jk7_61546/06_2025/9jk7_61546.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jk7_61546/06_2025/9jk7_61546.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jk7_61546/06_2025/9jk7_61546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jk7_61546/06_2025/9jk7_61546.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jk7_61546/06_2025/9jk7_61546.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jk7_61546/06_2025/9jk7_61546.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.037
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      60      5.16       5
     C   11706      2.51       5
     N    3084      2.21       5
     O    2970      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17820
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2970
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 16, 'TRANS': 345}
          Chain breaks: 2
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 7.57, per 1000 atoms: 0.42
  Number of scatterers: 17820
  At special positions: 0
  Unit cell: (97.37, 88.81, 217.21, 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      60     16.00
     O    2970      8.00
     N    3084      7.00
     C   11706      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 141 " - pdb=" SG  CYS C 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 141 " - pdb=" SG  CYS B 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 141 " - pdb=" SG  CYS E 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 141 " - pdb=" SG  CYS D 145 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 141 " - pdb=" SG  CYS F 145 " distance=2.03

  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: 4.39
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4212

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 6 sheets defined
      61.6% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 109 through 134
      Proline residue:  A 123  - end of helix
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 142 through 168
      removed outlier: 4.313A  pdb=" N   GLU A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE A 168 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 204
    Processing helix  chain 'A' and resid 211 through 238
      removed outlier: 3.748A  pdb=" N   VAL A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 283
      removed outlier: 4.740A  pdb=" N   HIS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 336
    Processing helix  chain 'A' and resid 339 through 369
    Processing helix  chain 'A' and resid 386 through 396
      removed outlier: 4.081A  pdb=" N   ALA A 396 " --> pdb=" O   GLN A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 409
    Processing helix  chain 'A' and resid 416 through 430
    Processing helix  chain 'A' and resid 433 through 443
      removed outlier: 4.917A  pdb=" N   ARG A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   TYR A 441 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 451 through 455
    Processing helix  chain 'B' and resid 110 through 134
      Proline residue:  B 123  - end of helix
      Proline residue:  B 130  - end of helix
    Processing helix  chain 'B' and resid 142 through 168
      removed outlier: 4.313A  pdb=" N   GLU B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE B 168 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 204
    Processing helix  chain 'B' and resid 211 through 238
      removed outlier: 3.749A  pdb=" N   VAL B 215 " --> pdb=" O   SER B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 283
      removed outlier: 4.740A  pdb=" N   HIS B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 336
    Processing helix  chain 'B' and resid 339 through 369
    Processing helix  chain 'B' and resid 386 through 396
      removed outlier: 4.081A  pdb=" N   ALA B 396 " --> pdb=" O   GLN B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 409
    Processing helix  chain 'B' and resid 416 through 430
    Processing helix  chain 'B' and resid 433 through 443
      removed outlier: 4.917A  pdb=" N   ARG B 440 " --> pdb=" O   ALA B 436 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   TYR B 441 " --> pdb=" O   PHE B 437 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 450
    Processing helix  chain 'B' and resid 451 through 455
    Processing helix  chain 'C' and resid 110 through 134
      Proline residue:  C 123  - end of helix
      Proline residue:  C 130  - end of helix
    Processing helix  chain 'C' and resid 142 through 168
      removed outlier: 4.313A  pdb=" N   GLU C 146 " --> pdb=" O   GLY C 142 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE C 168 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 204
    Processing helix  chain 'C' and resid 211 through 238
      removed outlier: 3.749A  pdb=" N   VAL C 215 " --> pdb=" O   SER C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 283
      removed outlier: 4.740A  pdb=" N   HIS C 281 " --> pdb=" O   GLU C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 336
    Processing helix  chain 'C' and resid 339 through 369
    Processing helix  chain 'C' and resid 386 through 396
      removed outlier: 4.081A  pdb=" N   ALA C 396 " --> pdb=" O   GLN C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 398 through 409
    Processing helix  chain 'C' and resid 416 through 430
    Processing helix  chain 'C' and resid 433 through 443
      removed outlier: 4.918A  pdb=" N   ARG C 440 " --> pdb=" O   ALA C 436 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   TYR C 441 " --> pdb=" O   PHE C 437 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA C 443 " --> pdb=" O   GLU C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 446 through 450
    Processing helix  chain 'C' and resid 451 through 455
    Processing helix  chain 'D' and resid 110 through 134
      Proline residue:  D 123  - end of helix
      Proline residue:  D 130  - end of helix
    Processing helix  chain 'D' and resid 142 through 168
      removed outlier: 4.314A  pdb=" N   GLU D 146 " --> pdb=" O   GLY D 142 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE D 168 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 204
    Processing helix  chain 'D' and resid 211 through 238
      removed outlier: 3.748A  pdb=" N   VAL D 215 " --> pdb=" O   SER D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 267 through 283
      removed outlier: 4.741A  pdb=" N   HIS D 281 " --> pdb=" O   GLU D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 336
    Processing helix  chain 'D' and resid 339 through 369
    Processing helix  chain 'D' and resid 386 through 396
      removed outlier: 4.081A  pdb=" N   ALA D 396 " --> pdb=" O   GLN D 392 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 398 through 409
    Processing helix  chain 'D' and resid 416 through 430
    Processing helix  chain 'D' and resid 433 through 443
      removed outlier: 4.917A  pdb=" N   ARG D 440 " --> pdb=" O   ALA D 436 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   TYR D 441 " --> pdb=" O   PHE D 437 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA D 443 " --> pdb=" O   GLU D 439 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 446 through 450
    Processing helix  chain 'D' and resid 451 through 455
    Processing helix  chain 'E' and resid 110 through 134
      Proline residue:  E 123  - end of helix
      Proline residue:  E 130  - end of helix
    Processing helix  chain 'E' and resid 142 through 168
      removed outlier: 4.314A  pdb=" N   GLU E 146 " --> pdb=" O   GLY E 142 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE E 168 " --> pdb=" O   TRP E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 204
    Processing helix  chain 'E' and resid 211 through 238
      removed outlier: 3.748A  pdb=" N   VAL E 215 " --> pdb=" O   SER E 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 267 through 283
      removed outlier: 4.740A  pdb=" N   HIS E 281 " --> pdb=" O   GLU E 277 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 327 through 336
    Processing helix  chain 'E' and resid 339 through 369
    Processing helix  chain 'E' and resid 386 through 396
      removed outlier: 4.081A  pdb=" N   ALA E 396 " --> pdb=" O   GLN E 392 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 398 through 409
    Processing helix  chain 'E' and resid 416 through 430
    Processing helix  chain 'E' and resid 433 through 443
      removed outlier: 4.917A  pdb=" N   ARG E 440 " --> pdb=" O   ALA E 436 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   TYR E 441 " --> pdb=" O   PHE E 437 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA E 443 " --> pdb=" O   GLU E 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 446 through 450
    Processing helix  chain 'E' and resid 451 through 455
    Processing helix  chain 'F' and resid 110 through 134
      Proline residue:  F 123  - end of helix
      Proline residue:  F 130  - end of helix
    Processing helix  chain 'F' and resid 142 through 168
      removed outlier: 4.314A  pdb=" N   GLU F 146 " --> pdb=" O   GLY F 142 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE F 168 " --> pdb=" O   TRP F 164 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 204
    Processing helix  chain 'F' and resid 211 through 238
      removed outlier: 3.748A  pdb=" N   VAL F 215 " --> pdb=" O   SER F 211 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 267 through 283
      removed outlier: 4.740A  pdb=" N   HIS F 281 " --> pdb=" O   GLU F 277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 327 through 336
    Processing helix  chain 'F' and resid 339 through 369
    Processing helix  chain 'F' and resid 386 through 396
      removed outlier: 4.081A  pdb=" N   ALA F 396 " --> pdb=" O   GLN F 392 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 398 through 409
    Processing helix  chain 'F' and resid 416 through 430
    Processing helix  chain 'F' and resid 433 through 443
      removed outlier: 4.917A  pdb=" N   ARG F 440 " --> pdb=" O   ALA F 436 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   TYR F 441 " --> pdb=" O   PHE F 437 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ALA F 443 " --> pdb=" O   GLU F 439 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 446 through 450
    Processing helix  chain 'F' and resid 451 through 455
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174
      removed outlier: 3.724A  pdb=" N   TRP A 460 " --> pdb=" O   LYS B 498 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER A 464 " --> pdb=" O   GLU B 502 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 173 through 174
      removed outlier: 6.739A  pdb=" N   PHE A 497 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LYS A 498 " --> pdb=" O   TRP C 460 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   LEU C 462 " --> pdb=" O   LYS A 498 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   SER A 500 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   SER C 464 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU A 502 " --> pdb=" O   SER C 464 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 174
      removed outlier: 3.638A  pdb=" N   TRP B 460 " --> pdb=" O   LYS C 498 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER B 464 " --> pdb=" O   GLU C 502 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 173 through 174
      removed outlier: 3.646A  pdb=" N   TRP D 460 " --> pdb=" O   LYS E 498 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER D 464 " --> pdb=" O   GLU E 502 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 173 through 174
      removed outlier: 6.742A  pdb=" N   PHE D 497 " --> pdb=" O   SER F 174 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   LYS D 498 " --> pdb=" O   TRP F 460 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU F 462 " --> pdb=" O   LYS D 498 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   SER D 500 " --> pdb=" O   LEU F 462 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   SER F 464 " --> pdb=" O   SER D 500 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLU D 502 " --> pdb=" O   SER F 464 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 173 through 174
      removed outlier: 3.565A  pdb=" N   TRP E 460 " --> pdb=" O   LYS F 498 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER E 464 " --> pdb=" O   GLU F 502 " (cutoff:3.500A)

    1095 hydrogen bonds defined for protein.
    3195 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: 5.60

  Time building geometry restraints manager: 5.22 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: 5579
        1.34 -     1.46: 2735
        1.46 -     1.57: 9854
        1.57 -     1.69: 0
        1.69 -     1.80: 102
  Bond restraints: 18270
  Sorted by residual:
  bond pdb=" CA  TYR B 450 "
       pdb=" C   TYR B 450 "
    ideal  model  delta    sigma   weight residual
    1.528  1.508  0.020 1.28e-02 6.10e+03 2.56e+00
  bond pdb=" CA  TYR A 450 "
       pdb=" C   TYR A 450 "
    ideal  model  delta    sigma   weight residual
    1.528  1.508  0.020 1.28e-02 6.10e+03 2.47e+00
  bond pdb=" CA  TYR F 450 "
       pdb=" C   TYR F 450 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.020 1.28e-02 6.10e+03 2.38e+00
  bond pdb=" CA  TYR C 450 "
       pdb=" C   TYR C 450 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.020 1.28e-02 6.10e+03 2.35e+00
  bond pdb=" CA  TYR D 450 "
       pdb=" C   TYR D 450 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.28e-02 6.10e+03 2.28e+00
  ... (remaining 18265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 23763
        1.46 -     2.92: 823
        2.92 -     4.38: 122
        4.38 -     5.84: 42
        5.84 -     7.30: 12
  Bond angle restraints: 24762
  Sorted by residual:
  angle pdb=" N   TYR B 450 "
        pdb=" CA  TYR B 450 "
        pdb=" C   TYR B 450 "
      ideal   model   delta    sigma   weight residual
     109.86  117.16   -7.30 1.55e+00 4.16e-01 2.22e+01
  angle pdb=" N   TYR C 450 "
        pdb=" CA  TYR C 450 "
        pdb=" C   TYR C 450 "
      ideal   model   delta    sigma   weight residual
     109.86  117.15   -7.29 1.55e+00 4.16e-01 2.21e+01
  angle pdb=" N   TYR A 450 "
        pdb=" CA  TYR A 450 "
        pdb=" C   TYR A 450 "
      ideal   model   delta    sigma   weight residual
     109.86  117.15   -7.29 1.55e+00 4.16e-01 2.21e+01
  angle pdb=" N   TYR F 450 "
        pdb=" CA  TYR F 450 "
        pdb=" C   TYR F 450 "
      ideal   model   delta    sigma   weight residual
     109.86  117.15   -7.29 1.55e+00 4.16e-01 2.21e+01
  angle pdb=" N   TYR D 450 "
        pdb=" CA  TYR D 450 "
        pdb=" C   TYR D 450 "
      ideal   model   delta    sigma   weight residual
     109.86  117.14   -7.28 1.55e+00 4.16e-01 2.21e+01
  ... (remaining 24757 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.50: 10098
       10.50 -    21.01: 672
       21.01 -    31.51: 110
       31.51 -    42.02: 40
       42.02 -    52.52: 12
  Dihedral angle restraints: 10932
    sinusoidal: 4476
      harmonic: 6456
  Sorted by residual:
  dihedral pdb=" CB  CYS D 141 "
           pdb=" SG  CYS D 141 "
           pdb=" SG  CYS D 145 "
           pdb=" CB  CYS D 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.52   52.52     1      1.00e+01 1.00e-02 3.76e+01
  dihedral pdb=" CB  CYS E 141 "
           pdb=" SG  CYS E 141 "
           pdb=" SG  CYS E 145 "
           pdb=" CB  CYS E 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.51   52.51     1      1.00e+01 1.00e-02 3.76e+01
  dihedral pdb=" CB  CYS A 141 "
           pdb=" SG  CYS A 141 "
           pdb=" SG  CYS A 145 "
           pdb=" CB  CYS A 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.49   52.49     1      1.00e+01 1.00e-02 3.75e+01
  ... (remaining 10929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 2333
       0.059 -    0.119: 432
       0.119 -    0.178: 37
       0.178 -    0.237: 0
       0.237 -    0.296: 6
  Chirality restraints: 2808
  Sorted by residual:
  chirality pdb=" CA  TYR A 450 "
            pdb=" N   TYR A 450 "
            pdb=" C   TYR A 450 "
            pdb=" CB  TYR A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  TYR F 450 "
            pdb=" N   TYR F 450 "
            pdb=" C   TYR F 450 "
            pdb=" CB  TYR F 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  TYR D 450 "
            pdb=" N   TYR D 450 "
            pdb=" C   TYR D 450 "
            pdb=" CB  TYR D 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.15e+00
  ... (remaining 2805 not shown)

  Planarity restraints: 3072
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 260 "   -0.011 2.00e-02 2.50e+03   1.82e-02 5.81e+00
        pdb=" CG  PHE B 260 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 260 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 260 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 260 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 260 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 260 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 260 "    0.011 2.00e-02 2.50e+03   1.82e-02 5.77e+00
        pdb=" CG  PHE C 260 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 260 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 260 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 260 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 260 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 260 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 260 "    0.011 2.00e-02 2.50e+03   1.80e-02 5.70e+00
        pdb=" CG  PHE E 260 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 260 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 260 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 260 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 260 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 260 "    0.000 2.00e-02 2.50e+03
  ... (remaining 3069 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 2740
        2.75 -     3.29: 17406
        3.29 -     3.83: 31400
        3.83 -     4.36: 37066
        4.36 -     4.90: 64594
  Nonbonded interactions: 153206
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 433 "
            pdb=" O   THR F 254 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR D 433 "
            pdb=" O   THR E 254 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR A 433 "
            pdb=" O   THR B 254 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   SER A 500 "
            pdb=" N   LEU C 462 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   SER D 500 "
            pdb=" N   LEU F 462 "
     model   vdw
     2.273 3.120
  ... (remaining 153201 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: 0.14
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.370
  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:          0.690
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     37.370
  Find NCS groups from input model:        0.370
  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:12.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
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      :  0.005   0.036  18276  Z= 0.202
  Angle     :  0.669   7.303  24774  Z= 0.375
  Chirality :  0.046   0.296   2808
  Planarity :  0.004   0.045   3072
  Dihedral  :  7.686  45.725   6702
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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: -0.76 (0.17), residues: 2136
  helix:  0.13 (0.14), residues: 1242
  sheet:  0.11 (0.38), residues: 186
  loop : -1.71 (0.21), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 164 
 HIS   0.008   0.001   HIS F 423 
 PHE   0.037   0.004   PHE B 260 
 TYR   0.022   0.002   TYR A 450 
 ARG   0.006   0.001   ARG E 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10587 ( 1095)
  hydrogen bonds       : angle       5.15878 ( 3195)
  SS BOND              : bond        0.00504 (    6)
  SS BOND              : angle       0.45044 (   12)
  covalent geometry    : bond        0.00468 (18270)
  covalent geometry    : angle       0.66929 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  444 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 444
  time to evaluate  : 1.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7389 (tp) cc_final: 0.7136 (mp)
REVERT: A  120 PHE cc_start: 0.7245 (t80) cc_final: 0.5751 (m-80)
REVERT: A  149 PHE cc_start: 0.7864 (m-80) cc_final: 0.7448 (m-10)
REVERT: A  243 GLN cc_start: 0.7922 (tt0) cc_final: 0.7596 (tt0)
REVERT: A  278 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8437 (mmtp)
REVERT: A  290 LEU cc_start: 0.8455 (mt) cc_final: 0.8188 (mp)
REVERT: A  385 MET cc_start: 0.8132 (ttp) cc_final: 0.7842 (ttm)
REVERT: A  404 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7846 (mmtt)
REVERT: A  452 LYS cc_start: 0.8202 (mttt) cc_final: 0.7169 (mppt)
REVERT: A  513 MET cc_start: 0.6483 (mmp) cc_final: 0.5387 (mmt)
REVERT: B  149 PHE cc_start: 0.7948 (m-80) cc_final: 0.7659 (m-80)
REVERT: B  186 MET cc_start: 0.7212 (mtt) cc_final: 0.6931 (mtp)
REVERT: B  208 ARG cc_start: 0.6196 (mtt-85) cc_final: 0.5793 (mtt180)
REVERT: B  245 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7761 (mp10)
REVERT: B  371 LYS cc_start: 0.7719 (tttt) cc_final: 0.7436 (ttpt)
REVERT: B  404 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7907 (mmtt)
REVERT: B  452 LYS cc_start: 0.8263 (mttt) cc_final: 0.7361 (mppt)
REVERT: B  473 LYS cc_start: 0.7651 (pttp) cc_final: 0.7288 (pttm)
REVERT: B  481 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7549 (mttt)
REVERT: C  118 LEU cc_start: 0.7538 (tp) cc_final: 0.7233 (mp)
REVERT: C  120 PHE cc_start: 0.7076 (t80) cc_final: 0.5422 (m-80)
REVERT: C  186 MET cc_start: 0.7146 (mtt) cc_final: 0.6864 (mtp)
REVERT: C  217 GLN cc_start: 0.7219 (mt0) cc_final: 0.6708 (mt0)
REVERT: C  273 VAL cc_start: 0.8479 (t) cc_final: 0.8262 (m)
REVERT: C  353 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7038 (mtm-85)
REVERT: C  371 LYS cc_start: 0.7808 (tttt) cc_final: 0.7577 (ttpt)
REVERT: C  404 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7770 (mmtt)
REVERT: C  452 LYS cc_start: 0.8271 (mttt) cc_final: 0.7411 (mppt)
REVERT: C  473 LYS cc_start: 0.7784 (pttp) cc_final: 0.7311 (pttm)
REVERT: C  513 MET cc_start: 0.6503 (mmp) cc_final: 0.5106 (mmt)
REVERT: D  118 LEU cc_start: 0.7451 (tp) cc_final: 0.7124 (mp)
REVERT: D  120 PHE cc_start: 0.7188 (t80) cc_final: 0.5728 (m-80)
REVERT: D  149 PHE cc_start: 0.7815 (m-80) cc_final: 0.7433 (m-10)
REVERT: D  290 LEU cc_start: 0.8458 (mt) cc_final: 0.8207 (mp)
REVERT: D  385 MET cc_start: 0.8145 (ttp) cc_final: 0.7852 (ttm)
REVERT: D  404 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7878 (mmtt)
REVERT: D  452 LYS cc_start: 0.8246 (mttt) cc_final: 0.7277 (mppt)
REVERT: D  513 MET cc_start: 0.6455 (mmp) cc_final: 0.5435 (mmt)
REVERT: E  120 PHE cc_start: 0.7153 (t80) cc_final: 0.5675 (m-80)
REVERT: E  186 MET cc_start: 0.7216 (mtt) cc_final: 0.6910 (mtp)
REVERT: E  217 GLN cc_start: 0.7182 (mt0) cc_final: 0.6667 (mt0)
REVERT: E  290 LEU cc_start: 0.8429 (mt) cc_final: 0.8100 (mt)
REVERT: E  371 LYS cc_start: 0.7749 (tttt) cc_final: 0.7459 (ttpt)
REVERT: E  404 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7936 (mmtt)
REVERT: E  452 LYS cc_start: 0.8256 (mttt) cc_final: 0.7280 (mppt)
REVERT: E  473 LYS cc_start: 0.7926 (pttp) cc_final: 0.7528 (pttm)
REVERT: E  513 MET cc_start: 0.6547 (mmp) cc_final: 0.5215 (mmp)
REVERT: F  118 LEU cc_start: 0.7470 (tp) cc_final: 0.7209 (mp)
REVERT: F  120 PHE cc_start: 0.7272 (t80) cc_final: 0.5553 (m-10)
REVERT: F  186 MET cc_start: 0.7134 (mtt) cc_final: 0.6904 (mtp)
REVERT: F  217 GLN cc_start: 0.7215 (mt0) cc_final: 0.6701 (mt0)
REVERT: F  278 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8348 (mmmt)
REVERT: F  353 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7050 (mtm-85)
REVERT: F  404 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7744 (mmtt)
REVERT: F  452 LYS cc_start: 0.8254 (mttt) cc_final: 0.7349 (mppt)
REVERT: F  473 LYS cc_start: 0.7909 (pttp) cc_final: 0.7450 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 444
  average time/residue: 1.6426
  time to fit residues: 800.0166
Evaluate side-chains
  281 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 4.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 182 optimal weight:    1.9990
   chunk 163 optimal weight:    0.6980
   chunk 90 optimal weight:    0.4980
   chunk 55 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 169 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 126 optimal weight:    0.5980
   chunk 196 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 339 ASN
A 403 GLN
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 470 ASN
B 217 GLN
** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 403 GLN
** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 339 ASN
** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 GLN
D 243 GLN
D 339 ASN
D 403 GLN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 470 ASN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 339 ASN
** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 339 ASN
** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.164612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.129207 restraints weight = 19174.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.60
r_work: 0.3283 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  18276  Z= 0.161
  Angle     :  0.589   7.564  24774  Z= 0.297
  Chirality :  0.043   0.183   2808
  Planarity :  0.004   0.040   3072
  Dihedral  :  4.384  19.148   2418
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.70 %
    Favored  : 88.34 %
  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:  0.83 (0.18), residues: 2136
  helix:  1.47 (0.14), residues: 1248
  sheet:  0.35 (0.39), residues: 186
  loop : -1.05 (0.22), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F 164 
 HIS   0.006   0.001   HIS A 423 
 PHE   0.021   0.003   PHE C 260 
 TYR   0.015   0.002   TYR B 342 
 ARG   0.005   0.000   ARG C 353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 ( 1095)
  hydrogen bonds       : angle       4.42405 ( 3195)
  SS BOND              : bond        0.00144 (    6)
  SS BOND              : angle       0.30329 (   12)
  covalent geometry    : bond        0.00376 (18270)
  covalent geometry    : angle       0.58960 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 323
  time to evaluate  : 2.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7519 (tp) cc_final: 0.7139 (mp)
REVERT: A  120 PHE cc_start: 0.7158 (t80) cc_final: 0.5468 (m-80)
REVERT: A  158 ILE cc_start: 0.8559 (mt) cc_final: 0.8325 (mm)
REVERT: A  170 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5911 (mmt-90)
REVERT: A  243 GLN cc_start: 0.8203 (tt0) cc_final: 0.7409 (tt0)
REVERT: A  245 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.6809 (mp10)
REVERT: A  333 ARG cc_start: 0.6908 (mtm180) cc_final: 0.6358 (tpm170)
REVERT: A  385 MET cc_start: 0.8250 (ttp) cc_final: 0.7752 (ttm)
REVERT: A  404 LYS cc_start: 0.8533 (mtpp) cc_final: 0.7934 (mmtt)
REVERT: A  452 LYS cc_start: 0.7726 (mttt) cc_final: 0.6387 (mppt)
REVERT: A  513 MET cc_start: 0.7207 (mmp) cc_final: 0.6455 (mmp)
REVERT: B  120 PHE cc_start: 0.6799 (t80) cc_final: 0.5126 (m-80)
REVERT: B  149 PHE cc_start: 0.7888 (m-80) cc_final: 0.7602 (m-80)
REVERT: B  177 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7601 (mtp180)
REVERT: B  186 MET cc_start: 0.7977 (mtt) cc_final: 0.7613 (mtp)
REVERT: B  341 TYR cc_start: 0.8611 (t80) cc_final: 0.8333 (t80)
REVERT: B  404 LYS cc_start: 0.8539 (mtpp) cc_final: 0.7908 (mmtt)
REVERT: B  473 LYS cc_start: 0.8043 (pttp) cc_final: 0.7469 (pttm)
REVERT: B  510 LYS cc_start: 0.7274 (mmtt) cc_final: 0.7073 (mmmm)
REVERT: C  120 PHE cc_start: 0.6954 (t80) cc_final: 0.5125 (m-80)
REVERT: C  160 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8401 (mt)
REVERT: C  186 MET cc_start: 0.8098 (mtt) cc_final: 0.7840 (mtp)
REVERT: C  255 ASP cc_start: 0.8397 (p0) cc_final: 0.8171 (p0)
REVERT: C  353 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7701 (mtt180)
REVERT: C  371 LYS cc_start: 0.7718 (tttt) cc_final: 0.7312 (ttpt)
REVERT: C  398 MET cc_start: 0.8800 (ptm) cc_final: 0.8591 (ptm)
REVERT: C  404 LYS cc_start: 0.8314 (mtpp) cc_final: 0.7785 (mmtt)
REVERT: C  417 MET cc_start: 0.7782 (tmm) cc_final: 0.7536 (tmm)
REVERT: C  470 ASN cc_start: 0.8144 (m110) cc_final: 0.7935 (m110)
REVERT: C  473 LYS cc_start: 0.8287 (pttp) cc_final: 0.7589 (pttm)
REVERT: C  502 GLU cc_start: 0.7227 (tt0) cc_final: 0.6885 (tp30)
REVERT: D  118 LEU cc_start: 0.7595 (tp) cc_final: 0.7241 (mt)
REVERT: D  120 PHE cc_start: 0.7099 (t80) cc_final: 0.5461 (m-80)
REVERT: D  158 ILE cc_start: 0.8578 (mt) cc_final: 0.8325 (mm)
REVERT: D  170 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6000 (mmt-90)
REVERT: D  290 LEU cc_start: 0.8504 (mt) cc_final: 0.8251 (mp)
REVERT: D  333 ARG cc_start: 0.6874 (mtm180) cc_final: 0.6361 (tpm170)
REVERT: D  385 MET cc_start: 0.8368 (ttp) cc_final: 0.7920 (ttm)
REVERT: D  404 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7939 (mmtt)
REVERT: D  452 LYS cc_start: 0.7779 (mttt) cc_final: 0.6448 (mppt)
REVERT: D  513 MET cc_start: 0.7208 (mmp) cc_final: 0.6089 (mmt)
REVERT: E  120 PHE cc_start: 0.6972 (t80) cc_final: 0.5373 (m-80)
REVERT: E  177 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7581 (mtp180)
REVERT: E  186 MET cc_start: 0.7995 (mtt) cc_final: 0.7637 (mtp)
REVERT: E  217 GLN cc_start: 0.7217 (mt0) cc_final: 0.6671 (mt0)
REVERT: E  290 LEU cc_start: 0.8445 (mt) cc_final: 0.8063 (mt)
REVERT: E  341 TYR cc_start: 0.8579 (t80) cc_final: 0.8369 (t80)
REVERT: E  354 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8080 (mtmm)
REVERT: E  403 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7460 (tm130)
REVERT: E  404 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7858 (mmtt)
REVERT: E  473 LYS cc_start: 0.8174 (pttp) cc_final: 0.7543 (pttm)
REVERT: E  502 GLU cc_start: 0.7551 (tt0) cc_final: 0.6973 (tp30)
REVERT: E  513 MET cc_start: 0.6988 (mmp) cc_final: 0.5705 (mmt)
REVERT: F  118 LEU cc_start: 0.7453 (tp) cc_final: 0.7048 (mp)
REVERT: F  120 PHE cc_start: 0.7006 (t80) cc_final: 0.5188 (m-80)
REVERT: F  160 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8414 (mt)
REVERT: F  186 MET cc_start: 0.8090 (mtt) cc_final: 0.7838 (mtp)
REVERT: F  255 ASP cc_start: 0.8404 (p0) cc_final: 0.8162 (p0)
REVERT: F  349 GLU cc_start: 0.7430 (tt0) cc_final: 0.7175 (tm-30)
REVERT: F  371 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7513 (mtpt)
REVERT: F  398 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8548 (ptm)
REVERT: F  404 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7791 (mmtt)
REVERT: F  416 THR cc_start: 0.8369 (p) cc_final: 0.8000 (t)
REVERT: F  473 LYS cc_start: 0.8251 (pttp) cc_final: 0.7548 (pttm)
REVERT: F  501 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7045 (tt0)
  outliers start: 37
  outliers final: 11
  residues processed: 341
  average time/residue: 1.4263
  time to fit residues: 538.8437
Evaluate side-chains
  305 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 286
  time to evaluate  : 1.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  513 MET
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  354 LYS
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  398 MET
Chi-restraints excluded: chain F residue  501 GLU
Chi-restraints excluded: chain F residue  513 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 112 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 185 optimal weight:    0.9980
   chunk 159 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 110 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 403 GLN
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 GLN
B 213 GLN
B 217 GLN
B 243 GLN
B 403 GLN
** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 GLN
C 217 GLN
** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 339 ASN
** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 GLN
D 403 GLN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 449 GLN
E 213 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 449 GLN
F 217 GLN
F 403 GLN
** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.162601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.126529 restraints weight = 19095.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.62
r_work: 0.3248 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  18276  Z= 0.168
  Angle     :  0.575   7.063  24774  Z= 0.288
  Chirality :  0.042   0.200   2808
  Planarity :  0.004   0.042   3072
  Dihedral  :  4.270  17.982   2418
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 11.66 %
    Favored  : 85.76 %
  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:  1.37 (0.18), residues: 2136
  helix:  1.87 (0.15), residues: 1248
  sheet:  0.50 (0.39), residues: 186
  loop : -0.73 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 164 
 HIS   0.006   0.001   HIS D 423 
 PHE   0.022   0.002   PHE E 367 
 TYR   0.015   0.002   TYR D 450 
 ARG   0.006   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03886 ( 1095)
  hydrogen bonds       : angle       4.33424 ( 3195)
  SS BOND              : bond        0.00041 (    6)
  SS BOND              : angle       0.27806 (   12)
  covalent geometry    : bond        0.00401 (18270)
  covalent geometry    : angle       0.57528 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 293
  time to evaluate  : 2.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7567 (tp) cc_final: 0.7166 (mp)
REVERT: A  120 PHE cc_start: 0.7112 (t80) cc_final: 0.5446 (m-80)
REVERT: A  158 ILE cc_start: 0.8523 (mt) cc_final: 0.8224 (mm)
REVERT: A  170 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6025 (mmt-90)
REVERT: A  243 GLN cc_start: 0.8208 (tt0) cc_final: 0.7461 (tt0)
REVERT: A  245 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.6954 (mp10)
REVERT: A  333 ARG cc_start: 0.6990 (mtm180) cc_final: 0.6368 (tpm170)
REVERT: A  385 MET cc_start: 0.8399 (ttp) cc_final: 0.7834 (ttm)
REVERT: A  404 LYS cc_start: 0.8511 (mtpp) cc_final: 0.7904 (mmtt)
REVERT: A  418 GLU cc_start: 0.7871 (tp30) cc_final: 0.7560 (tp30)
REVERT: A  452 LYS cc_start: 0.7574 (mttt) cc_final: 0.6327 (mppt)
REVERT: A  473 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7585 (pttm)
REVERT: B  120 PHE cc_start: 0.6885 (t80) cc_final: 0.5135 (m-80)
REVERT: B  149 PHE cc_start: 0.7830 (m-80) cc_final: 0.7510 (m-80)
REVERT: B  177 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7504 (mtp180)
REVERT: B  186 MET cc_start: 0.8084 (mtt) cc_final: 0.7694 (mtp)
REVERT: B  341 TYR cc_start: 0.8606 (t80) cc_final: 0.8314 (t80)
REVERT: B  365 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7230 (mp0)
REVERT: B  388 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.6755 (ttt90)
REVERT: B  404 LYS cc_start: 0.8519 (mtpp) cc_final: 0.7877 (mmtt)
REVERT: B  473 LYS cc_start: 0.8082 (pttp) cc_final: 0.7493 (pttm)
REVERT: C  120 PHE cc_start: 0.6863 (t80) cc_final: 0.5106 (m-80)
REVERT: C  148 LEU cc_start: 0.7832 (mt) cc_final: 0.7622 (mp)
REVERT: C  186 MET cc_start: 0.8129 (mtt) cc_final: 0.7894 (mtp)
REVERT: C  245 GLN cc_start: 0.8590 (mm110) cc_final: 0.8372 (mm110)
REVERT: C  255 ASP cc_start: 0.8460 (p0) cc_final: 0.8245 (p0)
REVERT: C  349 GLU cc_start: 0.7365 (tt0) cc_final: 0.7103 (tt0)
REVERT: C  353 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7820 (mtm110)
REVERT: C  371 LYS cc_start: 0.7746 (tttt) cc_final: 0.7333 (ttpt)
REVERT: C  404 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7734 (mmtt)
REVERT: C  417 MET cc_start: 0.7811 (tmm) cc_final: 0.7510 (tmm)
REVERT: C  473 LYS cc_start: 0.8205 (pttp) cc_final: 0.7516 (pttm)
REVERT: C  502 GLU cc_start: 0.7270 (tt0) cc_final: 0.6913 (tp30)
REVERT: C  513 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7295 (tpp)
REVERT: D  118 LEU cc_start: 0.7594 (tp) cc_final: 0.7240 (mt)
REVERT: D  120 PHE cc_start: 0.7074 (t80) cc_final: 0.5429 (m-80)
REVERT: D  158 ILE cc_start: 0.8540 (mt) cc_final: 0.8244 (mm)
REVERT: D  170 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6012 (mmt-90)
REVERT: D  245 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.6827 (mp10)
REVERT: D  290 LEU cc_start: 0.8604 (mt) cc_final: 0.8354 (mp)
REVERT: D  333 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6356 (tpm170)
REVERT: D  385 MET cc_start: 0.8362 (ttp) cc_final: 0.7750 (ttm)
REVERT: D  404 LYS cc_start: 0.8448 (mtpp) cc_final: 0.7915 (mmtt)
REVERT: D  418 GLU cc_start: 0.7858 (tp30) cc_final: 0.7546 (tp30)
REVERT: D  452 LYS cc_start: 0.7667 (mttt) cc_final: 0.6410 (mppt)
REVERT: D  473 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7571 (pttm)
REVERT: D  513 MET cc_start: 0.7314 (mmp) cc_final: 0.6313 (mmt)
REVERT: E  120 PHE cc_start: 0.6973 (t80) cc_final: 0.5369 (m-80)
REVERT: E  177 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7529 (mtp180)
REVERT: E  186 MET cc_start: 0.8054 (mtt) cc_final: 0.7661 (mtp)
REVERT: E  217 GLN cc_start: 0.7214 (mt0) cc_final: 0.6693 (mt0)
REVERT: E  290 LEU cc_start: 0.8471 (mt) cc_final: 0.8088 (mt)
REVERT: E  341 TYR cc_start: 0.8561 (t80) cc_final: 0.8341 (t80)
REVERT: E  365 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7172 (mp0)
REVERT: E  371 LYS cc_start: 0.7899 (tttt) cc_final: 0.7372 (ttpt)
REVERT: E  388 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6541 (ttt90)
REVERT: E  404 LYS cc_start: 0.8522 (mtpp) cc_final: 0.7859 (mmtt)
REVERT: E  473 LYS cc_start: 0.8126 (pttp) cc_final: 0.7551 (pttm)
REVERT: E  502 GLU cc_start: 0.7513 (tt0) cc_final: 0.6960 (tp30)
REVERT: F  120 PHE cc_start: 0.6895 (t80) cc_final: 0.5076 (m-80)
REVERT: F  177 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7533 (mtp180)
REVERT: F  186 MET cc_start: 0.8113 (mtt) cc_final: 0.7888 (mtp)
REVERT: F  217 GLN cc_start: 0.7208 (mt0) cc_final: 0.6636 (mt0)
REVERT: F  255 ASP cc_start: 0.8459 (p0) cc_final: 0.8249 (p0)
REVERT: F  371 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7539 (mtpt)
REVERT: F  388 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6710 (ttt90)
REVERT: F  398 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8471 (ptm)
REVERT: F  404 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7769 (mmtt)
REVERT: F  422 GLN cc_start: 0.7632 (mt0) cc_final: 0.7046 (mm110)
REVERT: F  473 LYS cc_start: 0.8197 (pttp) cc_final: 0.7515 (pttm)
REVERT: F  501 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6981 (tt0)
REVERT: F  502 GLU cc_start: 0.7270 (tt0) cc_final: 0.6880 (tp30)
REVERT: F  513 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7104 (mmm)
  outliers start: 49
  outliers final: 13
  residues processed: 316
  average time/residue: 1.5762
  time to fit residues: 546.8964
Evaluate side-chains
  306 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 281
  time to evaluate  : 1.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  513 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  365 GLU
Chi-restraints excluded: chain E residue  388 ARG
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  388 ARG
Chi-restraints excluded: chain F residue  398 MET
Chi-restraints excluded: chain F residue  501 GLU
Chi-restraints excluded: chain F residue  513 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 185 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 102 optimal weight:    0.5980
   chunk 215 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 191 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 403 GLN
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 GLN
B 217 GLN
B 243 GLN
B 403 GLN
** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN
** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 GLN
D 403 GLN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 403 GLN
** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.178061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.146568 restraints weight = 19605.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.48
r_work: 0.3542 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  18276  Z= 0.147
  Angle     :  0.544   6.917  24774  Z= 0.273
  Chirality :  0.041   0.145   2808
  Planarity :  0.004   0.042   3072
  Dihedral  :  4.114  17.302   2418
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.18 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.18), residues: 2136
  helix:  2.16 (0.15), residues: 1248
  sheet:  0.62 (0.40), residues: 186
  loop : -0.57 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 423 
 PHE   0.017   0.002   PHE E 367 
 TYR   0.012   0.002   TYR A 450 
 ARG   0.005   0.000   ARG F 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 ( 1095)
  hydrogen bonds       : angle       4.24588 ( 3195)
  SS BOND              : bond        0.00034 (    6)
  SS BOND              : angle       0.27726 (   12)
  covalent geometry    : bond        0.00347 (18270)
  covalent geometry    : angle       0.54432 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 302
  time to evaluate  : 2.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7686 (tp) cc_final: 0.7345 (mt)
REVERT: A  120 PHE cc_start: 0.7166 (t80) cc_final: 0.5594 (m-80)
REVERT: A  158 ILE cc_start: 0.8649 (mt) cc_final: 0.8379 (mm)
REVERT: A  170 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6227 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8182 (m-80) cc_final: 0.7488 (m-80)
REVERT: A  243 GLN cc_start: 0.8213 (tt0) cc_final: 0.7515 (tt0)
REVERT: A  245 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7007 (mp10)
REVERT: A  333 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6493 (tpm170)
REVERT: A  371 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7495 (ttpt)
REVERT: A  385 MET cc_start: 0.8481 (ttp) cc_final: 0.7906 (ttm)
REVERT: A  404 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8138 (mmtt)
REVERT: A  452 LYS cc_start: 0.7663 (mttt) cc_final: 0.6535 (mppt)
REVERT: A  473 LYS cc_start: 0.8373 (ptmt) cc_final: 0.7816 (pttm)
REVERT: B  120 PHE cc_start: 0.6898 (t80) cc_final: 0.5228 (m-80)
REVERT: B  149 PHE cc_start: 0.7993 (m-80) cc_final: 0.7732 (m-80)
REVERT: B  177 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7627 (mtp180)
REVERT: B  186 MET cc_start: 0.8189 (mtt) cc_final: 0.7856 (mtp)
REVERT: B  341 TYR cc_start: 0.8660 (t80) cc_final: 0.8429 (t80)
REVERT: B  365 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7408 (mp0)
REVERT: B  388 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.6805 (ttt90)
REVERT: B  398 MET cc_start: 0.8892 (ptm) cc_final: 0.8618 (ptm)
REVERT: B  404 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8113 (mmtt)
REVERT: B  473 LYS cc_start: 0.8237 (pttp) cc_final: 0.7690 (pttm)
REVERT: C  120 PHE cc_start: 0.6898 (t80) cc_final: 0.5164 (m-80)
REVERT: C  160 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8574 (mt)
REVERT: C  217 GLN cc_start: 0.7392 (mt0) cc_final: 0.6830 (mt0)
REVERT: C  371 LYS cc_start: 0.8002 (tttt) cc_final: 0.7606 (ttpt)
REVERT: C  404 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8007 (mmtt)
REVERT: C  417 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7571 (tmm)
REVERT: C  473 LYS cc_start: 0.8322 (pttp) cc_final: 0.7729 (pttm)
REVERT: C  502 GLU cc_start: 0.7284 (tt0) cc_final: 0.7019 (tp30)
REVERT: D  118 LEU cc_start: 0.7729 (tp) cc_final: 0.7329 (mt)
REVERT: D  120 PHE cc_start: 0.7148 (t80) cc_final: 0.5581 (m-80)
REVERT: D  158 ILE cc_start: 0.8661 (mt) cc_final: 0.8383 (mm)
REVERT: D  170 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6207 (mmt-90)
REVERT: D  196 TYR cc_start: 0.7969 (m-80) cc_final: 0.7680 (m-80)
REVERT: D  245 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.6879 (mp10)
REVERT: D  290 LEU cc_start: 0.8626 (mt) cc_final: 0.8362 (mp)
REVERT: D  333 ARG cc_start: 0.7035 (mtm180) cc_final: 0.6437 (tpm170)
REVERT: D  349 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7598 (mp0)
REVERT: D  371 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7541 (ttpt)
REVERT: D  385 MET cc_start: 0.8467 (ttp) cc_final: 0.7891 (ttm)
REVERT: D  404 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8091 (mmtt)
REVERT: D  418 GLU cc_start: 0.7852 (tp30) cc_final: 0.7643 (tp30)
REVERT: D  452 LYS cc_start: 0.7676 (mttt) cc_final: 0.6541 (mppt)
REVERT: D  473 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7788 (pttm)
REVERT: E  118 LEU cc_start: 0.7137 (mp) cc_final: 0.6793 (tt)
REVERT: E  120 PHE cc_start: 0.6923 (t80) cc_final: 0.5435 (m-80)
REVERT: E  177 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7625 (mtp180)
REVERT: E  186 MET cc_start: 0.8187 (mtt) cc_final: 0.7857 (mtp)
REVERT: E  217 GLN cc_start: 0.7362 (mt0) cc_final: 0.6861 (mt0)
REVERT: E  290 LEU cc_start: 0.8486 (mt) cc_final: 0.8136 (mt)
REVERT: E  365 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7380 (mp0)
REVERT: E  371 LYS cc_start: 0.7835 (tttt) cc_final: 0.7364 (ttpt)
REVERT: E  388 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6564 (ttt90)
REVERT: E  404 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8078 (mmtt)
REVERT: E  473 LYS cc_start: 0.8249 (pttp) cc_final: 0.7738 (pttm)
REVERT: E  502 GLU cc_start: 0.7399 (tt0) cc_final: 0.7069 (tp30)
REVERT: F  120 PHE cc_start: 0.6895 (t80) cc_final: 0.5164 (m-80)
REVERT: F  160 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8577 (mt)
REVERT: F  177 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7592 (mtp180)
REVERT: F  217 GLN cc_start: 0.7258 (mt0) cc_final: 0.6706 (mt0)
REVERT: F  371 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7671 (mtpt)
REVERT: F  404 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7997 (mmtt)
REVERT: F  473 LYS cc_start: 0.8346 (pttp) cc_final: 0.7818 (pttm)
REVERT: F  502 GLU cc_start: 0.7295 (tt0) cc_final: 0.7037 (tp30)
  outliers start: 56
  outliers final: 21
  residues processed: 330
  average time/residue: 1.5750
  time to fit residues: 572.5068
Evaluate side-chains
  324 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 293
  time to evaluate  : 1.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  417 MET
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  365 GLU
Chi-restraints excluded: chain E residue  388 ARG
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  282 ASP
Chi-restraints excluded: chain F residue  466 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 101 optimal weight:    0.0980
   chunk 175 optimal weight:    0.1980
   chunk 92 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 145 optimal weight:    1.9990
   chunk 205 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 185 optimal weight:    0.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 403 GLN
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 GLN
B 217 GLN
B 403 GLN
B 470 ASN
C 213 GLN
D 217 GLN
D 245 GLN
D 403 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 403 GLN
F 403 GLN
F 470 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.177292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.145493 restraints weight = 19698.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 1.49
r_work: 0.3529 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  18276  Z= 0.159
  Angle     :  0.552   7.045  24774  Z= 0.276
  Chirality :  0.041   0.155   2808
  Planarity :  0.004   0.045   3072
  Dihedral  :  4.119  16.508   2418
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 12.39 %
    Favored  : 84.34 %
  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:  1.82 (0.18), residues: 2136
  helix:  2.22 (0.15), residues: 1248
  sheet:  0.69 (0.41), residues: 186
  loop : -0.51 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 274 
 HIS   0.004   0.001   HIS D 423 
 PHE   0.017   0.002   PHE E 367 
 TYR   0.016   0.002   TYR D 280 
 ARG   0.004   0.000   ARG C 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 ( 1095)
  hydrogen bonds       : angle       4.24486 ( 3195)
  SS BOND              : bond        0.00018 (    6)
  SS BOND              : angle       0.25642 (   12)
  covalent geometry    : bond        0.00379 (18270)
  covalent geometry    : angle       0.55246 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 293
  time to evaluate  : 1.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7733 (tp) cc_final: 0.7298 (mp)
REVERT: A  120 PHE cc_start: 0.7206 (t80) cc_final: 0.5599 (m-80)
REVERT: A  158 ILE cc_start: 0.8652 (mt) cc_final: 0.8370 (mm)
REVERT: A  170 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6200 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8169 (m-80) cc_final: 0.7639 (m-80)
REVERT: A  243 GLN cc_start: 0.8152 (tt0) cc_final: 0.7495 (tt0)
REVERT: A  245 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7024 (mp10)
REVERT: A  333 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6505 (tpm170)
REVERT: A  349 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7575 (mp0)
REVERT: A  371 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7532 (ttmt)
REVERT: A  385 MET cc_start: 0.8479 (ttp) cc_final: 0.7871 (ttm)
REVERT: A  404 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8109 (mmtt)
REVERT: A  452 LYS cc_start: 0.7678 (mttt) cc_final: 0.6547 (mppt)
REVERT: A  473 LYS cc_start: 0.8381 (ptmt) cc_final: 0.7823 (pttm)
REVERT: B  120 PHE cc_start: 0.6915 (t80) cc_final: 0.5216 (m-80)
REVERT: B  177 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7652 (mtp180)
REVERT: B  186 MET cc_start: 0.8225 (mtt) cc_final: 0.7866 (mtp)
REVERT: B  217 GLN cc_start: 0.7396 (mt0) cc_final: 0.6903 (mt0)
REVERT: B  341 TYR cc_start: 0.8693 (t80) cc_final: 0.8471 (t80)
REVERT: B  365 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7406 (mp0)
REVERT: B  388 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.6823 (ttt90)
REVERT: B  398 MET cc_start: 0.8877 (ptm) cc_final: 0.8632 (ptm)
REVERT: B  404 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8090 (mmtt)
REVERT: B  473 LYS cc_start: 0.8227 (pttp) cc_final: 0.7738 (pttm)
REVERT: C  120 PHE cc_start: 0.7017 (t80) cc_final: 0.5205 (m-80)
REVERT: C  160 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8585 (mt)
REVERT: C  177 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7576 (mtp180)
REVERT: C  217 GLN cc_start: 0.7380 (mt0) cc_final: 0.6826 (mt0)
REVERT: C  371 LYS cc_start: 0.8054 (tttt) cc_final: 0.7691 (ttpt)
REVERT: C  404 LYS cc_start: 0.8412 (mtpp) cc_final: 0.7986 (mmtt)
REVERT: C  417 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7669 (tmm)
REVERT: C  473 LYS cc_start: 0.8330 (pttp) cc_final: 0.7738 (pttm)
REVERT: C  502 GLU cc_start: 0.7296 (tt0) cc_final: 0.7060 (tp30)
REVERT: D  118 LEU cc_start: 0.7740 (tp) cc_final: 0.7384 (mt)
REVERT: D  120 PHE cc_start: 0.7167 (t80) cc_final: 0.5577 (m-80)
REVERT: D  158 ILE cc_start: 0.8672 (mt) cc_final: 0.8386 (mm)
REVERT: D  196 TYR cc_start: 0.8030 (m-80) cc_final: 0.7750 (m-80)
REVERT: D  290 LEU cc_start: 0.8551 (mt) cc_final: 0.8297 (mp)
REVERT: D  333 ARG cc_start: 0.7112 (mtm180) cc_final: 0.6476 (tpm170)
REVERT: D  371 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7568 (ttmt)
REVERT: D  385 MET cc_start: 0.8475 (ttp) cc_final: 0.7858 (ttm)
REVERT: D  404 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8112 (mmtt)
REVERT: D  452 LYS cc_start: 0.7701 (mttt) cc_final: 0.6561 (mppt)
REVERT: D  473 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7766 (pttm)
REVERT: E  118 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6824 (tt)
REVERT: E  120 PHE cc_start: 0.6951 (t80) cc_final: 0.5447 (m-80)
REVERT: E  177 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7669 (mtp180)
REVERT: E  186 MET cc_start: 0.8211 (mtt) cc_final: 0.7847 (mtp)
REVERT: E  217 GLN cc_start: 0.7362 (mt0) cc_final: 0.6852 (mt0)
REVERT: E  290 LEU cc_start: 0.8524 (mt) cc_final: 0.8166 (mt)
REVERT: E  365 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7403 (mp0)
REVERT: E  371 LYS cc_start: 0.7873 (tttt) cc_final: 0.7429 (ttpt)
REVERT: E  388 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6606 (ttt90)
REVERT: E  404 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8041 (mmtt)
REVERT: E  465 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7276 (pt0)
REVERT: E  473 LYS cc_start: 0.8238 (pttp) cc_final: 0.7739 (pttm)
REVERT: E  502 GLU cc_start: 0.7509 (tt0) cc_final: 0.7093 (tp30)
REVERT: F  120 PHE cc_start: 0.7006 (t80) cc_final: 0.5203 (m-80)
REVERT: F  160 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8591 (mt)
REVERT: F  177 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7663 (mtp180)
REVERT: F  217 GLN cc_start: 0.7343 (mt0) cc_final: 0.6788 (mt0)
REVERT: F  404 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8013 (mmtt)
REVERT: F  473 LYS cc_start: 0.8360 (pttp) cc_final: 0.7843 (pttm)
REVERT: F  501 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7210 (tt0)
  outliers start: 62
  outliers final: 23
  residues processed: 328
  average time/residue: 1.5442
  time to fit residues: 556.1814
Evaluate side-chains
  321 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 287
  time to evaluate  : 2.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  417 MET
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain D residue  513 MET
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  365 GLU
Chi-restraints excluded: chain E residue  388 ARG
Chi-restraints excluded: chain E residue  465 GLU
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  282 ASP
Chi-restraints excluded: chain F residue  501 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 212 optimal weight:    1.9990
   chunk 135 optimal weight:    0.5980
   chunk 155 optimal weight:    0.9990
   chunk 52 optimal weight:    0.3980
   chunk 115 optimal weight:    0.8980
   chunk 143 optimal weight:    0.7980
   chunk 215 optimal weight:    0.9990
   chunk 65 optimal weight:    0.2980
   chunk 99 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 403 GLN
B 213 GLN
B 243 GLN
B 403 GLN
B 470 ASN
C 213 GLN
D 217 GLN
D 245 GLN
D 403 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 470 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.169784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.135338 restraints weight = 19531.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.51
r_work: 0.3372 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  18276  Z= 0.152
  Angle     :  0.543   7.052  24774  Z= 0.272
  Chirality :  0.041   0.160   2808
  Planarity :  0.004   0.046   3072
  Dihedral  :  4.067  16.202   2418
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.92 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.94 (0.18), residues: 2136
  helix:  2.29 (0.14), residues: 1248
  sheet:  0.97 (0.41), residues: 180
  loop : -0.46 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 274 
 HIS   0.004   0.001   HIS A 423 
 PHE   0.015   0.002   PHE E 367 
 TYR   0.016   0.002   TYR D 280 
 ARG   0.005   0.000   ARG C 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 ( 1095)
  hydrogen bonds       : angle       4.23751 ( 3195)
  SS BOND              : bond        0.00022 (    6)
  SS BOND              : angle       0.27603 (   12)
  covalent geometry    : bond        0.00362 (18270)
  covalent geometry    : angle       0.54269 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 287
  time to evaluate  : 1.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7752 (tp) cc_final: 0.7316 (mp)
REVERT: A  120 PHE cc_start: 0.7212 (t80) cc_final: 0.5511 (m-80)
REVERT: A  158 ILE cc_start: 0.8682 (mt) cc_final: 0.8394 (mm)
REVERT: A  170 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6175 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8182 (m-80) cc_final: 0.7590 (m-80)
REVERT: A  243 GLN cc_start: 0.8104 (tt0) cc_final: 0.7456 (tt0)
REVERT: A  245 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7081 (mp10)
REVERT: A  333 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6528 (tpm170)
REVERT: A  371 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7497 (ttmt)
REVERT: A  385 MET cc_start: 0.8422 (ttp) cc_final: 0.7699 (ttm)
REVERT: A  404 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8088 (mmtt)
REVERT: A  452 LYS cc_start: 0.7764 (mttt) cc_final: 0.6679 (mppt)
REVERT: A  473 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7783 (pttm)
REVERT: B  120 PHE cc_start: 0.6923 (t80) cc_final: 0.5208 (m-80)
REVERT: B  177 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7667 (mtp180)
REVERT: B  186 MET cc_start: 0.8214 (mtt) cc_final: 0.7862 (mtp)
REVERT: B  217 GLN cc_start: 0.7264 (mt0) cc_final: 0.6750 (mt0)
REVERT: B  341 TYR cc_start: 0.8701 (t80) cc_final: 0.8463 (t80)
REVERT: B  365 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7438 (mp0)
REVERT: B  388 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.6856 (ttt90)
REVERT: B  398 MET cc_start: 0.8962 (ptm) cc_final: 0.8683 (ptm)
REVERT: B  404 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8020 (mmtt)
REVERT: B  473 LYS cc_start: 0.8206 (pttp) cc_final: 0.7729 (pttm)
REVERT: C  120 PHE cc_start: 0.7001 (t80) cc_final: 0.5187 (m-80)
REVERT: C  160 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8588 (mt)
REVERT: C  177 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7624 (mtp180)
REVERT: C  217 GLN cc_start: 0.7356 (mt0) cc_final: 0.6787 (mt0)
REVERT: C  371 LYS cc_start: 0.8100 (tttt) cc_final: 0.7755 (ttpt)
REVERT: C  404 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7934 (mmtt)
REVERT: C  417 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7732 (tmm)
REVERT: C  473 LYS cc_start: 0.8285 (pttp) cc_final: 0.7757 (pttm)
REVERT: C  513 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7756 (mmm)
REVERT: D  118 LEU cc_start: 0.7758 (tp) cc_final: 0.7353 (mt)
REVERT: D  120 PHE cc_start: 0.7132 (t80) cc_final: 0.5484 (m-80)
REVERT: D  158 ILE cc_start: 0.8680 (mt) cc_final: 0.8398 (mm)
REVERT: D  170 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6091 (mmt-90)
REVERT: D  196 TYR cc_start: 0.8084 (m-80) cc_final: 0.7702 (m-80)
REVERT: D  290 LEU cc_start: 0.8544 (mt) cc_final: 0.8279 (mp)
REVERT: D  333 ARG cc_start: 0.7173 (mtm180) cc_final: 0.6478 (tpm170)
REVERT: D  371 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7541 (ttmt)
REVERT: D  385 MET cc_start: 0.8414 (ttp) cc_final: 0.7690 (ttm)
REVERT: D  398 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (ptm)
REVERT: D  404 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8068 (mmtt)
REVERT: D  452 LYS cc_start: 0.7763 (mttt) cc_final: 0.6623 (mppt)
REVERT: D  473 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7741 (pttm)
REVERT: E  118 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6787 (tt)
REVERT: E  120 PHE cc_start: 0.6921 (t80) cc_final: 0.5377 (m-80)
REVERT: E  177 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7683 (mtp180)
REVERT: E  186 MET cc_start: 0.8214 (mtt) cc_final: 0.7932 (mtp)
REVERT: E  217 GLN cc_start: 0.7379 (mt0) cc_final: 0.6884 (mt0)
REVERT: E  290 LEU cc_start: 0.8497 (mt) cc_final: 0.8130 (mt)
REVERT: E  388 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6637 (ttt90)
REVERT: E  398 MET cc_start: 0.8727 (ptp) cc_final: 0.8519 (ptm)
REVERT: E  404 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8031 (mmtt)
REVERT: E  473 LYS cc_start: 0.8200 (pttp) cc_final: 0.7717 (pttm)
REVERT: E  502 GLU cc_start: 0.7430 (tt0) cc_final: 0.7084 (tp30)
REVERT: E  513 MET cc_start: 0.8180 (mmm) cc_final: 0.7936 (mmm)
REVERT: F  120 PHE cc_start: 0.6979 (t80) cc_final: 0.5158 (m-80)
REVERT: F  160 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8597 (mt)
REVERT: F  177 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7703 (mtp180)
REVERT: F  217 GLN cc_start: 0.7254 (mt0) cc_final: 0.6691 (mt0)
REVERT: F  371 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7647 (mtmt)
REVERT: F  404 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7978 (mmtt)
REVERT: F  473 LYS cc_start: 0.8271 (pttp) cc_final: 0.7851 (pttm)
REVERT: F  513 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7727 (mmm)
  outliers start: 57
  outliers final: 22
  residues processed: 315
  average time/residue: 1.5818
  time to fit residues: 546.3742
Evaluate side-chains
  319 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 285
  time to evaluate  : 1.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  417 MET
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain C residue  513 MET
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  398 MET
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  388 ARG
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  282 ASP
Chi-restraints excluded: chain F residue  513 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 195 optimal weight:    0.8980
   chunk 207 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0970
   chunk 106 optimal weight:    0.6980
   chunk 187 optimal weight:    0.7980
   chunk 135 optimal weight:    0.4980
   chunk 125 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 156 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 403 GLN
B 213 GLN
B 403 GLN
B 470 ASN
D 217 GLN
D 245 GLN
D 403 GLN
D 411 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 403 GLN
F 470 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.169314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.134604 restraints weight = 19614.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.56
r_work: 0.3364 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  18276  Z= 0.140
  Angle     :  0.529   7.109  24774  Z= 0.265
  Chirality :  0.040   0.141   2808
  Planarity :  0.004   0.045   3072
  Dihedral  :  3.997  15.413   2418
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 13.34 %
    Favored  : 83.60 %
  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:  2.03 (0.18), residues: 2136
  helix:  2.36 (0.14), residues: 1248
  sheet:  1.01 (0.41), residues: 180
  loop : -0.42 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 423 
 PHE   0.015   0.002   PHE F 149 
 TYR   0.014   0.001   TYR A 280 
 ARG   0.005   0.000   ARG C 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 ( 1095)
  hydrogen bonds       : angle       4.20756 ( 3195)
  SS BOND              : bond        0.00029 (    6)
  SS BOND              : angle       0.26411 (   12)
  covalent geometry    : bond        0.00332 (18270)
  covalent geometry    : angle       0.52879 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 292
  time to evaluate  : 1.998 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7739 (tp) cc_final: 0.7293 (mp)
REVERT: A  120 PHE cc_start: 0.7121 (t80) cc_final: 0.5480 (m-80)
REVERT: A  158 ILE cc_start: 0.8668 (mt) cc_final: 0.8375 (mm)
REVERT: A  170 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6102 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8205 (m-80) cc_final: 0.7605 (m-80)
REVERT: A  243 GLN cc_start: 0.8041 (tt0) cc_final: 0.7414 (tt0)
REVERT: A  245 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7102 (mp10)
REVERT: A  385 MET cc_start: 0.8419 (ttp) cc_final: 0.7861 (ttm)
REVERT: A  388 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7697 (ttm-80)
REVERT: A  404 LYS cc_start: 0.8525 (mtpp) cc_final: 0.8054 (mmtt)
REVERT: A  452 LYS cc_start: 0.7746 (mttt) cc_final: 0.6654 (mppt)
REVERT: A  473 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7758 (pttm)
REVERT: B  120 PHE cc_start: 0.6913 (t80) cc_final: 0.5191 (m-80)
REVERT: B  177 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7583 (mtp180)
REVERT: B  186 MET cc_start: 0.8198 (mtt) cc_final: 0.7917 (mtp)
REVERT: B  217 GLN cc_start: 0.7244 (mt0) cc_final: 0.6715 (mt0)
REVERT: B  341 TYR cc_start: 0.8672 (t80) cc_final: 0.8459 (t80)
REVERT: B  365 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7432 (mp0)
REVERT: B  388 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.6821 (ttt90)
REVERT: B  398 MET cc_start: 0.8951 (ptm) cc_final: 0.8671 (ptm)
REVERT: B  404 LYS cc_start: 0.8608 (mtpp) cc_final: 0.7995 (mmtt)
REVERT: B  473 LYS cc_start: 0.8210 (pttp) cc_final: 0.7730 (pttm)
REVERT: C  120 PHE cc_start: 0.7003 (t80) cc_final: 0.5149 (m-80)
REVERT: C  126 PHE cc_start: 0.8167 (m-10) cc_final: 0.7963 (m-10)
REVERT: C  160 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8566 (mt)
REVERT: C  177 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7585 (mtp180)
REVERT: C  217 GLN cc_start: 0.7328 (mt0) cc_final: 0.6755 (mt0)
REVERT: C  339 ASN cc_start: 0.8132 (t0) cc_final: 0.7927 (t160)
REVERT: C  371 LYS cc_start: 0.8081 (tttt) cc_final: 0.7738 (ttpt)
REVERT: C  404 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7901 (mmtt)
REVERT: C  473 LYS cc_start: 0.8323 (pttp) cc_final: 0.7811 (pttm)
REVERT: D  118 LEU cc_start: 0.7746 (tp) cc_final: 0.7338 (mt)
REVERT: D  120 PHE cc_start: 0.7119 (t80) cc_final: 0.5457 (m-80)
REVERT: D  158 ILE cc_start: 0.8677 (mt) cc_final: 0.8386 (mm)
REVERT: D  170 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6030 (mmt-90)
REVERT: D  196 TYR cc_start: 0.8080 (m-80) cc_final: 0.7699 (m-80)
REVERT: D  290 LEU cc_start: 0.8530 (mt) cc_final: 0.8259 (mp)
REVERT: D  333 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6495 (tpm170)
REVERT: D  371 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7532 (ttmt)
REVERT: D  385 MET cc_start: 0.8410 (ttp) cc_final: 0.7765 (ttm)
REVERT: D  388 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7666 (ttm-80)
REVERT: D  398 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (ptm)
REVERT: D  404 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8012 (mmtt)
REVERT: D  452 LYS cc_start: 0.7775 (mttt) cc_final: 0.6669 (mppt)
REVERT: D  473 LYS cc_start: 0.8251 (ptmt) cc_final: 0.7728 (pttm)
REVERT: E  118 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6776 (tt)
REVERT: E  120 PHE cc_start: 0.6870 (t80) cc_final: 0.5325 (m-80)
REVERT: E  177 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7604 (mtp180)
REVERT: E  186 MET cc_start: 0.8201 (mtt) cc_final: 0.7888 (mtp)
REVERT: E  217 GLN cc_start: 0.7338 (mt0) cc_final: 0.6828 (mt0)
REVERT: E  290 LEU cc_start: 0.8476 (mt) cc_final: 0.8119 (mt)
REVERT: E  371 LYS cc_start: 0.7735 (tttt) cc_final: 0.7281 (ttpt)
REVERT: E  404 LYS cc_start: 0.8603 (mtpp) cc_final: 0.7986 (mmtt)
REVERT: E  473 LYS cc_start: 0.8204 (pttp) cc_final: 0.7710 (pttm)
REVERT: E  502 GLU cc_start: 0.7444 (tt0) cc_final: 0.7072 (tp30)
REVERT: F  120 PHE cc_start: 0.6979 (t80) cc_final: 0.5130 (m-80)
REVERT: F  126 PHE cc_start: 0.8209 (m-10) cc_final: 0.7999 (m-10)
REVERT: F  160 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8579 (mt)
REVERT: F  177 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7677 (mtp180)
REVERT: F  217 GLN cc_start: 0.7229 (mt0) cc_final: 0.6663 (mt0)
REVERT: F  339 ASN cc_start: 0.8134 (t0) cc_final: 0.7912 (t160)
REVERT: F  371 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7784 (mtmt)
REVERT: F  404 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7940 (mmtt)
REVERT: F  452 LYS cc_start: 0.7931 (mttt) cc_final: 0.6603 (mppt)
REVERT: F  473 LYS cc_start: 0.8268 (pttp) cc_final: 0.7838 (pttm)
  outliers start: 58
  outliers final: 23
  residues processed: 317
  average time/residue: 1.5183
  time to fit residues: 529.7652
Evaluate side-chains
  321 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 288
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  388 ARG
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  398 MET
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  384 VAL
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  349 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 164 optimal weight:    2.9990
   chunk 159 optimal weight:    0.8980
   chunk 125 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9980
   chunk 119 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0970
   chunk 10 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 206 optimal weight:    0.5980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 217 GLN
A 403 GLN
B 213 GLN
B 403 GLN
B 470 ASN
D 217 GLN
D 245 GLN
D 403 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 470 ASN
F 470 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.167886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.134405 restraints weight = 19662.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.47
r_work: 0.3351 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  18276  Z= 0.166
  Angle     :  0.563   9.075  24774  Z= 0.278
  Chirality :  0.041   0.168   2808
  Planarity :  0.004   0.047   3072
  Dihedral  :  4.073  17.367   2418
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.08 %
    Favored  : 83.33 %
  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:  1.93 (0.18), residues: 2136
  helix:  2.28 (0.14), residues: 1248
  sheet:  0.72 (0.41), residues: 186
  loop : -0.40 (0.24), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 274 
 HIS   0.007   0.001   HIS F 348 
 PHE   0.020   0.002   PHE F 149 
 TYR   0.018   0.002   TYR F 280 
 ARG   0.005   0.000   ARG F 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 ( 1095)
  hydrogen bonds       : angle       4.24472 ( 3195)
  SS BOND              : bond        0.00028 (    6)
  SS BOND              : angle       0.27258 (   12)
  covalent geometry    : bond        0.00398 (18270)
  covalent geometry    : angle       0.56264 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 293
  time to evaluate  : 2.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7751 (tp) cc_final: 0.7306 (mp)
REVERT: A  120 PHE cc_start: 0.7218 (t80) cc_final: 0.5485 (m-80)
REVERT: A  158 ILE cc_start: 0.8674 (mt) cc_final: 0.8378 (mm)
REVERT: A  170 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6114 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8200 (m-80) cc_final: 0.7603 (m-80)
REVERT: A  243 GLN cc_start: 0.8023 (tt0) cc_final: 0.7391 (tt0)
REVERT: A  245 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7080 (mp10)
REVERT: A  388 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7681 (ttm-80)
REVERT: A  404 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8049 (mmtt)
REVERT: A  452 LYS cc_start: 0.7755 (mttt) cc_final: 0.6674 (mppt)
REVERT: A  473 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7783 (pttm)
REVERT: A  513 MET cc_start: 0.7921 (tpp) cc_final: 0.7674 (tpt)
REVERT: B  120 PHE cc_start: 0.6916 (t80) cc_final: 0.5179 (m-80)
REVERT: B  177 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7643 (mtp180)
REVERT: B  186 MET cc_start: 0.8207 (mtt) cc_final: 0.7882 (mtp)
REVERT: B  217 GLN cc_start: 0.7237 (mt0) cc_final: 0.6720 (mt0)
REVERT: B  341 TYR cc_start: 0.8708 (t80) cc_final: 0.8487 (t80)
REVERT: B  365 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7426 (mp0)
REVERT: B  388 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.6825 (ttt90)
REVERT: B  398 MET cc_start: 0.8955 (ptm) cc_final: 0.8689 (ptm)
REVERT: B  404 LYS cc_start: 0.8621 (mtpp) cc_final: 0.7989 (mmtt)
REVERT: B  473 LYS cc_start: 0.8244 (pttp) cc_final: 0.7745 (pttm)
REVERT: C  120 PHE cc_start: 0.6895 (t80) cc_final: 0.5153 (m-80)
REVERT: C  126 PHE cc_start: 0.8231 (m-10) cc_final: 0.7822 (m-10)
REVERT: C  160 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8576 (mt)
REVERT: C  177 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7574 (mtp180)
REVERT: C  217 GLN cc_start: 0.7324 (mt0) cc_final: 0.6749 (mt0)
REVERT: C  339 ASN cc_start: 0.8098 (t0) cc_final: 0.7876 (t160)
REVERT: C  371 LYS cc_start: 0.8097 (tttt) cc_final: 0.7824 (ttpt)
REVERT: C  404 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7922 (mmtt)
REVERT: C  473 LYS cc_start: 0.8273 (pttp) cc_final: 0.7755 (pttm)
REVERT: D  118 LEU cc_start: 0.7770 (tp) cc_final: 0.7368 (mt)
REVERT: D  120 PHE cc_start: 0.7229 (t80) cc_final: 0.5467 (m-80)
REVERT: D  158 ILE cc_start: 0.8674 (mt) cc_final: 0.8383 (mm)
REVERT: D  170 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6042 (mmt-90)
REVERT: D  177 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7582 (mtp180)
REVERT: D  196 TYR cc_start: 0.8082 (m-80) cc_final: 0.7627 (m-80)
REVERT: D  290 LEU cc_start: 0.8549 (mt) cc_final: 0.8277 (mp)
REVERT: D  371 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7540 (ttmt)
REVERT: D  385 MET cc_start: 0.8363 (ttp) cc_final: 0.7793 (ttm)
REVERT: D  388 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7714 (ttm-80)
REVERT: D  404 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8015 (mmtt)
REVERT: D  452 LYS cc_start: 0.7821 (mttt) cc_final: 0.6682 (mppt)
REVERT: D  473 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7773 (pttm)
REVERT: E  118 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6778 (tt)
REVERT: E  120 PHE cc_start: 0.6929 (t80) cc_final: 0.5331 (m-80)
REVERT: E  177 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7672 (mtp180)
REVERT: E  186 MET cc_start: 0.8205 (mtt) cc_final: 0.7874 (mtp)
REVERT: E  217 GLN cc_start: 0.7353 (mt0) cc_final: 0.6855 (mt0)
REVERT: E  290 LEU cc_start: 0.8485 (mt) cc_final: 0.8112 (mt)
REVERT: E  388 ARG cc_start: 0.7849 (ttt90) cc_final: 0.6761 (ttt90)
REVERT: E  404 LYS cc_start: 0.8606 (mtpp) cc_final: 0.7970 (mmtt)
REVERT: E  473 LYS cc_start: 0.8250 (pttp) cc_final: 0.7738 (pttm)
REVERT: E  502 GLU cc_start: 0.7460 (tt0) cc_final: 0.7050 (tp30)
REVERT: F  120 PHE cc_start: 0.6905 (t80) cc_final: 0.5162 (m-80)
REVERT: F  126 PHE cc_start: 0.8239 (m-10) cc_final: 0.7798 (m-10)
REVERT: F  160 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8579 (mt)
REVERT: F  177 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7697 (mtp180)
REVERT: F  217 GLN cc_start: 0.7300 (mt0) cc_final: 0.6730 (mt0)
REVERT: F  339 ASN cc_start: 0.8131 (t0) cc_final: 0.7929 (t160)
REVERT: F  371 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7736 (mtmt)
REVERT: F  404 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7971 (mmtt)
REVERT: F  452 LYS cc_start: 0.8033 (mttt) cc_final: 0.6693 (mppt)
REVERT: F  473 LYS cc_start: 0.8279 (pttp) cc_final: 0.7854 (pttm)
  outliers start: 49
  outliers final: 22
  residues processed: 316
  average time/residue: 1.5902
  time to fit residues: 552.6773
Evaluate side-chains
  321 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 289
  time to evaluate  : 1.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  388 ARG
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  282 ASP
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  282 ASP
Chi-restraints excluded: chain F residue  371 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 133 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 209 optimal weight:    0.0870
   chunk 61 optimal weight:    1.9990
   chunk 214 optimal weight:    0.6980
   chunk 151 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 178 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 217 GLN
A 403 GLN
B 213 GLN
B 403 GLN
B 470 ASN
D 217 GLN
D 245 GLN
D 403 GLN
D 422 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 470 ASN
F 470 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.169609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.135029 restraints weight = 19740.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.56
r_work: 0.3382 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18276  Z= 0.135
  Angle     :  0.534   8.256  24774  Z= 0.267
  Chirality :  0.040   0.163   2808
  Planarity :  0.004   0.046   3072
  Dihedral  :  3.964  17.274   2418
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.66 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.18), residues: 2136
  helix:  2.39 (0.14), residues: 1248
  sheet:  1.03 (0.42), residues: 180
  loop : -0.41 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 423 
 PHE   0.020   0.002   PHE F 149 
 TYR   0.013   0.001   TYR F 280 
 ARG   0.006   0.000   ARG C 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 ( 1095)
  hydrogen bonds       : angle       4.19910 ( 3195)
  SS BOND              : bond        0.00032 (    6)
  SS BOND              : angle       0.27734 (   12)
  covalent geometry    : bond        0.00318 (18270)
  covalent geometry    : angle       0.53453 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 300
  time to evaluate  : 2.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7790 (tp) cc_final: 0.7436 (mt)
REVERT: A  120 PHE cc_start: 0.7168 (t80) cc_final: 0.5449 (m-80)
REVERT: A  158 ILE cc_start: 0.8669 (mt) cc_final: 0.8371 (mm)
REVERT: A  170 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6099 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8241 (m-80) cc_final: 0.7650 (m-80)
REVERT: A  243 GLN cc_start: 0.8027 (tt0) cc_final: 0.7357 (tt0)
REVERT: A  245 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7086 (mp10)
REVERT: A  385 MET cc_start: 0.8549 (ttp) cc_final: 0.8185 (ttm)
REVERT: A  388 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7725 (ttm-80)
REVERT: A  404 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8063 (mmtt)
REVERT: A  452 LYS cc_start: 0.7772 (mttt) cc_final: 0.6637 (mppt)
REVERT: A  473 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7780 (pttm)
REVERT: A  513 MET cc_start: 0.7930 (tpp) cc_final: 0.7696 (tpt)
REVERT: B  120 PHE cc_start: 0.6910 (t80) cc_final: 0.5192 (m-80)
REVERT: B  177 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7587 (mtp180)
REVERT: B  186 MET cc_start: 0.8194 (mtt) cc_final: 0.7882 (mtp)
REVERT: B  217 GLN cc_start: 0.7236 (mt0) cc_final: 0.6742 (mt0)
REVERT: B  341 TYR cc_start: 0.8655 (t80) cc_final: 0.8425 (t80)
REVERT: B  365 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7397 (mp0)
REVERT: B  388 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.6836 (ttt90)
REVERT: B  398 MET cc_start: 0.8948 (ptm) cc_final: 0.8696 (ptm)
REVERT: B  404 LYS cc_start: 0.8589 (mtpp) cc_final: 0.7962 (mmtt)
REVERT: B  473 LYS cc_start: 0.8237 (pttp) cc_final: 0.7751 (pttm)
REVERT: C  120 PHE cc_start: 0.6856 (t80) cc_final: 0.5138 (m-80)
REVERT: C  126 PHE cc_start: 0.8176 (m-10) cc_final: 0.7935 (m-10)
REVERT: C  160 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8561 (mt)
REVERT: C  177 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7582 (mtp180)
REVERT: C  217 GLN cc_start: 0.7337 (mt0) cc_final: 0.6739 (mt0)
REVERT: C  339 ASN cc_start: 0.8068 (t0) cc_final: 0.7857 (t160)
REVERT: C  341 TYR cc_start: 0.8530 (t80) cc_final: 0.8317 (t80)
REVERT: C  371 LYS cc_start: 0.8054 (tttt) cc_final: 0.7785 (ttpt)
REVERT: C  404 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7931 (mmtt)
REVERT: C  473 LYS cc_start: 0.8313 (pttp) cc_final: 0.7853 (pttm)
REVERT: D  118 LEU cc_start: 0.7743 (tp) cc_final: 0.7330 (mt)
REVERT: D  120 PHE cc_start: 0.7190 (t80) cc_final: 0.5444 (m-80)
REVERT: D  149 PHE cc_start: 0.7674 (m-80) cc_final: 0.7212 (m-10)
REVERT: D  158 ILE cc_start: 0.8668 (mt) cc_final: 0.8373 (mm)
REVERT: D  170 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6039 (mmt-90)
REVERT: D  196 TYR cc_start: 0.8110 (m-80) cc_final: 0.7739 (m-80)
REVERT: D  290 LEU cc_start: 0.8528 (mt) cc_final: 0.8244 (mp)
REVERT: D  333 ARG cc_start: 0.7392 (mtm180) cc_final: 0.6536 (tpm170)
REVERT: D  371 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7501 (ttmt)
REVERT: D  385 MET cc_start: 0.8386 (ttp) cc_final: 0.7838 (ttm)
REVERT: D  388 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7729 (ttm-80)
REVERT: D  404 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8028 (mmtt)
REVERT: D  452 LYS cc_start: 0.7807 (mttt) cc_final: 0.6662 (mppt)
REVERT: D  473 LYS cc_start: 0.8298 (ptmt) cc_final: 0.7749 (pttm)
REVERT: E  118 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6777 (tt)
REVERT: E  120 PHE cc_start: 0.6864 (t80) cc_final: 0.5320 (m-80)
REVERT: E  177 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7608 (mtp180)
REVERT: E  186 MET cc_start: 0.8190 (mtt) cc_final: 0.7877 (mtp)
REVERT: E  217 GLN cc_start: 0.7342 (mt0) cc_final: 0.6866 (mt0)
REVERT: E  290 LEU cc_start: 0.8447 (mt) cc_final: 0.8073 (mt)
REVERT: E  371 LYS cc_start: 0.7709 (tttt) cc_final: 0.7279 (ttpt)
REVERT: E  388 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6765 (ttt90)
REVERT: E  404 LYS cc_start: 0.8580 (mtpp) cc_final: 0.7949 (mmtt)
REVERT: E  473 LYS cc_start: 0.8211 (pttp) cc_final: 0.7719 (pttm)
REVERT: E  502 GLU cc_start: 0.7431 (tt0) cc_final: 0.7004 (tp30)
REVERT: F  120 PHE cc_start: 0.6848 (t80) cc_final: 0.5128 (m-80)
REVERT: F  160 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8573 (mt)
REVERT: F  177 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7672 (mtp180)
REVERT: F  217 GLN cc_start: 0.7239 (mt0) cc_final: 0.6641 (mt0)
REVERT: F  339 ASN cc_start: 0.8020 (t0) cc_final: 0.7810 (t160)
REVERT: F  371 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7735 (mtmt)
REVERT: F  404 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7958 (mmtt)
REVERT: F  452 LYS cc_start: 0.7965 (mttt) cc_final: 0.6657 (mppt)
REVERT: F  473 LYS cc_start: 0.8287 (pttp) cc_final: 0.7866 (pttm)
  outliers start: 43
  outliers final: 22
  residues processed: 320
  average time/residue: 1.5230
  time to fit residues: 537.0715
Evaluate side-chains
  325 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 292
  time to evaluate  : 1.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  388 ARG
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  365 GLU
Chi-restraints excluded: chain E residue  384 VAL
Chi-restraints excluded: chain E residue  388 ARG
Chi-restraints excluded: chain E residue  418 GLU
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  371 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 172 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 177 optimal weight:    0.6980
   chunk 68 optimal weight:    0.4980
   chunk 130 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 217 GLN
A 403 GLN
A 411 GLN
B 213 GLN
B 403 GLN
B 470 ASN
C 213 GLN
D 213 GLN
D 217 GLN
D 245 GLN
D 403 GLN
D 422 GLN
E 213 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 470 ASN
F 213 GLN
F 470 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.167661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.132832 restraints weight = 19745.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.56
r_work: 0.3332 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  18276  Z= 0.168
  Angle     :  0.569   8.273  24774  Z= 0.283
  Chirality :  0.042   0.196   2808
  Planarity :  0.004   0.047   3072
  Dihedral  :  4.094  17.557   2418
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.24 %
    Favored  : 82.81 %
  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:  1.96 (0.18), residues: 2136
  helix:  2.26 (0.14), residues: 1248
  sheet:  0.98 (0.42), residues: 180
  loop : -0.38 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 164 
 HIS   0.004   0.001   HIS A 423 
 PHE   0.025   0.002   PHE F 149 
 TYR   0.019   0.002   TYR F 280 
 ARG   0.006   0.000   ARG F 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 ( 1095)
  hydrogen bonds       : angle       4.27264 ( 3195)
  SS BOND              : bond        0.00033 (    6)
  SS BOND              : angle       0.26404 (   12)
  covalent geometry    : bond        0.00403 (18270)
  covalent geometry    : angle       0.56908 (24762)

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

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

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4272 Ramachandran restraints generated.
    2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 286
  time to evaluate  : 1.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LEU cc_start: 0.7773 (tp) cc_final: 0.7323 (mp)
REVERT: A  120 PHE cc_start: 0.7217 (t80) cc_final: 0.5486 (m-80)
REVERT: A  158 ILE cc_start: 0.8663 (mt) cc_final: 0.8361 (mm)
REVERT: A  170 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6118 (mmt-90)
REVERT: A  196 TYR cc_start: 0.8236 (m-80) cc_final: 0.7636 (m-80)
REVERT: A  243 GLN cc_start: 0.8036 (tt0) cc_final: 0.7423 (tt0)
REVERT: A  245 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7081 (mp10)
REVERT: A  385 MET cc_start: 0.8564 (ttp) cc_final: 0.8214 (ttm)
REVERT: A  388 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7719 (ttm-80)
REVERT: A  404 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8087 (mmtt)
REVERT: A  452 LYS cc_start: 0.7824 (mttt) cc_final: 0.6630 (mppt)
REVERT: A  473 LYS cc_start: 0.8286 (ptmt) cc_final: 0.7772 (pttm)
REVERT: B  120 PHE cc_start: 0.6959 (t80) cc_final: 0.5250 (m-80)
REVERT: B  177 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7682 (mtp180)
REVERT: B  186 MET cc_start: 0.8238 (mtt) cc_final: 0.7917 (mtp)
REVERT: B  341 TYR cc_start: 0.8718 (t80) cc_final: 0.8489 (t80)
REVERT: B  365 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7436 (mp0)
REVERT: B  388 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.6830 (ttt90)
REVERT: B  404 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8009 (mmtt)
REVERT: B  473 LYS cc_start: 0.8243 (pttp) cc_final: 0.7755 (pttm)
REVERT: C  120 PHE cc_start: 0.6961 (t80) cc_final: 0.5219 (m-80)
REVERT: C  126 PHE cc_start: 0.8209 (m-10) cc_final: 0.7790 (m-10)
REVERT: C  160 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8572 (mt)
REVERT: C  177 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7600 (mtp180)
REVERT: C  217 GLN cc_start: 0.7327 (mt0) cc_final: 0.6737 (mt0)
REVERT: C  339 ASN cc_start: 0.8119 (t0) cc_final: 0.7896 (t160)
REVERT: C  371 LYS cc_start: 0.8119 (tttt) cc_final: 0.7856 (ttpt)
REVERT: C  404 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7914 (mmtt)
REVERT: C  452 LYS cc_start: 0.7972 (mttt) cc_final: 0.6704 (mppt)
REVERT: C  473 LYS cc_start: 0.8264 (pttp) cc_final: 0.7726 (pttm)
REVERT: D  118 LEU cc_start: 0.7788 (tp) cc_final: 0.7379 (mt)
REVERT: D  120 PHE cc_start: 0.7253 (t80) cc_final: 0.5489 (m-80)
REVERT: D  149 PHE cc_start: 0.7680 (m-80) cc_final: 0.7205 (m-10)
REVERT: D  158 ILE cc_start: 0.8682 (mt) cc_final: 0.8391 (mm)
REVERT: D  170 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6124 (mmt-90)
REVERT: D  196 TYR cc_start: 0.8122 (m-80) cc_final: 0.7680 (m-80)
REVERT: D  290 LEU cc_start: 0.8538 (mt) cc_final: 0.8254 (mp)
REVERT: D  333 ARG cc_start: 0.7408 (mtm180) cc_final: 0.6551 (tpm170)
REVERT: D  371 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7545 (ttmt)
REVERT: D  385 MET cc_start: 0.8426 (ttp) cc_final: 0.7861 (ttm)
REVERT: D  388 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7735 (ttm-80)
REVERT: D  404 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8082 (mmtt)
REVERT: D  452 LYS cc_start: 0.7868 (mttt) cc_final: 0.6661 (mppt)
REVERT: D  473 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7768 (pttm)
REVERT: E  118 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6796 (tt)
REVERT: E  120 PHE cc_start: 0.6840 (t80) cc_final: 0.5387 (m-80)
REVERT: E  177 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7706 (mtp180)
REVERT: E  186 MET cc_start: 0.8199 (mtt) cc_final: 0.7867 (mtp)
REVERT: E  217 GLN cc_start: 0.7376 (mt0) cc_final: 0.6864 (mt0)
REVERT: E  371 LYS cc_start: 0.7783 (tttt) cc_final: 0.7368 (ttpt)
REVERT: E  388 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6607 (ttt90)
REVERT: E  404 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7992 (mmtt)
REVERT: E  473 LYS cc_start: 0.8256 (pttp) cc_final: 0.7750 (pttm)
REVERT: E  502 GLU cc_start: 0.7513 (tt0) cc_final: 0.7092 (tp30)
REVERT: F  120 PHE cc_start: 0.6903 (t80) cc_final: 0.5183 (m-80)
REVERT: F  160 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8588 (mt)
REVERT: F  177 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7739 (mtp180)
REVERT: F  217 GLN cc_start: 0.7304 (mt0) cc_final: 0.6723 (mt0)
REVERT: F  339 ASN cc_start: 0.8131 (t0) cc_final: 0.7917 (t160)
REVERT: F  371 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7825 (mtmt)
REVERT: F  404 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7911 (mmtt)
REVERT: F  452 LYS cc_start: 0.7945 (mttt) cc_final: 0.6662 (mppt)
REVERT: F  473 LYS cc_start: 0.8293 (pttp) cc_final: 0.7872 (pttm)
  outliers start: 37
  outliers final: 14
  residues processed: 303
  average time/residue: 1.6493
  time to fit residues: 548.8176
Evaluate side-chains
  309 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 284
  time to evaluate  : 2.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  170 ARG
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  245 GLN
Chi-restraints excluded: chain A residue  388 ARG
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain D residue  152 VAL
Chi-restraints excluded: chain D residue  170 ARG
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  388 ARG
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  388 ARG
Chi-restraints excluded: chain E residue  492 LYS
Chi-restraints excluded: chain F residue  118 LEU
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  371 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 101 optimal weight:    0.0060
   chunk 167 optimal weight:    0.9980
   chunk 191 optimal weight:    0.6980
   chunk 162 optimal weight:    0.9980
   chunk 134 optimal weight:    0.9980
   chunk 184 optimal weight:    0.9990
   chunk 203 optimal weight:    0.9980
   chunk 154 optimal weight:    6.9990
   chunk 80 optimal weight:    0.5980
   chunk 113 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 217 GLN
A 403 GLN
B 213 GLN
B 217 GLN
B 403 GLN
B 470 ASN
C 213 GLN
C 470 ASN
D 213 GLN
D 217 GLN
D 245 GLN
D 403 GLN
D 422 GLN
E 213 GLN
** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 470 ASN
F 213 GLN
F 470 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.167962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.133282 restraints weight = 19700.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.55
r_work: 0.3349 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  18276  Z= 0.163
  Angle     :  0.566   9.900  24774  Z= 0.282
  Chirality :  0.042   0.218   2808
  Planarity :  0.004   0.047   3072
  Dihedral  :  4.090  17.224   2418
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.51 %
    Favored  : 82.54 %
  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:  1.96 (0.18), residues: 2136
  helix:  2.25 (0.14), residues: 1248
  sheet:  0.99 (0.41), residues: 180
  loop : -0.35 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 274 
 HIS   0.004   0.001   HIS A 423 
 PHE   0.027   0.002   PHE F 149 
 TYR   0.018   0.002   TYR F 280 
 ARG   0.006   0.000   ARG C 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 ( 1095)
  hydrogen bonds       : angle       4.28572 ( 3195)
  SS BOND              : bond        0.00028 (    6)
  SS BOND              : angle       0.28587 (   12)
  covalent geometry    : bond        0.00390 (18270)
  covalent geometry    : angle       0.56617 (24762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15729.08 seconds
wall clock time: 272 minutes 42.58 seconds (16362.58 seconds total)