Starting phenix.real_space_refine
on Thu Sep 18 08:16:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eky_48141/09_2025/9eky_48141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eky_48141/09_2025/9eky_48141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eky_48141/09_2025/9eky_48141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eky_48141/09_2025/9eky_48141.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eky_48141/09_2025/9eky_48141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eky_48141/09_2025/9eky_48141.map"
  }
  resolution = 2.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.030
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      96      5.16       5
     C   10020      2.51       5
     N    2412      2.21       5
     O    2688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15216
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 3774
          Classifications: {'peptide': 459}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 451}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'ZB4': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.38, per 1000 atoms: 0.22
  Number of scatterers: 15216
  At special positions: 0
  Unit cell: (115.128, 115.128, 117.936, 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      96     16.00
     O    2688      8.00
     N    2412      7.00
     C   10020      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 243 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 164 " - pdb=" SG  CYS B 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 164 " - pdb=" SG  CYS C 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 164 " - pdb=" SG  CYS D 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 243 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 243 " - pdb=" SG  CYS C 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 243 " - pdb=" SG  CYS D 274 " 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: 1.32
  Conformation dependent library (CDL) restraints added in 673.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3512

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 8 sheets defined
      66.3% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 49
    Processing helix  chain 'A' and resid 51 through 60
      removed outlier: 3.533A  pdb=" N   ARG A  57 " --> pdb=" O   CYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 106
    Processing helix  chain 'A' and resid 123 through 140
    Processing helix  chain 'A' and resid 141 through 144
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 3.634A  pdb=" N   ARG A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.635A  pdb=" N   SER A 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 329
      removed outlier: 3.716A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 371
      removed outlier: 3.519A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 398
      removed outlier: 3.552A  pdb=" N   LEU A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 394 " --> pdb=" O   TRP A 390 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG A 395 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 411
    Processing helix  chain 'A' and resid 412 through 440
      removed outlier: 4.655A  pdb=" N   LYS A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   MET A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE A 427 " --> pdb=" O   CYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
      removed outlier: 3.882A  pdb=" N   GLU A 447 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 464 through 472
      removed outlier: 4.408A  pdb=" N   ILE A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 517
      removed outlier: 3.755A  pdb=" N   ASP A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 49
    Processing helix  chain 'B' and resid 51 through 60
      removed outlier: 3.533A  pdb=" N   ARG B  57 " --> pdb=" O   CYS B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 106
    Processing helix  chain 'B' and resid 123 through 140
    Processing helix  chain 'B' and resid 141 through 144
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 208 through 212
      removed outlier: 3.634A  pdb=" N   ARG B 212 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 238
      removed outlier: 3.635A  pdb=" N   SER B 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 329
      removed outlier: 3.716A  pdb=" N   LYS B 329 " --> pdb=" O   PHE B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 371
      removed outlier: 3.519A  pdb=" N   LEU B 349 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 398
      removed outlier: 3.552A  pdb=" N   LEU B 388 " --> pdb=" O   THR B 384 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 394 " --> pdb=" O   TRP B 390 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG B 395 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR B 396 " --> pdb=" O   GLY B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 412 through 440
      removed outlier: 4.656A  pdb=" N   LYS B 416 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   MET B 426 " --> pdb=" O   ALA B 422 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE B 427 " --> pdb=" O   CYS B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 447
      removed outlier: 3.882A  pdb=" N   GLU B 447 " --> pdb=" O   ASP B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 461
    Processing helix  chain 'B' and resid 464 through 472
      removed outlier: 4.408A  pdb=" N   ILE B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 517
      removed outlier: 3.755A  pdb=" N   ASP B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 49
    Processing helix  chain 'C' and resid 51 through 60
      removed outlier: 3.533A  pdb=" N   ARG C  57 " --> pdb=" O   CYS C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 106
    Processing helix  chain 'C' and resid 123 through 140
    Processing helix  chain 'C' and resid 141 through 144
    Processing helix  chain 'C' and resid 195 through 200
    Processing helix  chain 'C' and resid 208 through 212
      removed outlier: 3.634A  pdb=" N   ARG C 212 " --> pdb=" O   SER C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 238
      removed outlier: 3.635A  pdb=" N   SER C 237 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 329
      removed outlier: 3.716A  pdb=" N   LYS C 329 " --> pdb=" O   PHE C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 371
      removed outlier: 3.519A  pdb=" N   LEU C 349 " --> pdb=" O   GLY C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 398
      removed outlier: 3.552A  pdb=" N   LEU C 388 " --> pdb=" O   THR C 384 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE C 394 " --> pdb=" O   TRP C 390 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG C 395 " --> pdb=" O   VAL C 391 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR C 396 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 411
    Processing helix  chain 'C' and resid 412 through 440
      removed outlier: 4.655A  pdb=" N   LYS C 416 " --> pdb=" O   ALA C 412 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   MET C 426 " --> pdb=" O   ALA C 422 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE C 427 " --> pdb=" O   CYS C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 447
      removed outlier: 3.882A  pdb=" N   GLU C 447 " --> pdb=" O   ASP C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 461
    Processing helix  chain 'C' and resid 464 through 472
      removed outlier: 4.408A  pdb=" N   ILE C 472 " --> pdb=" O   THR C 468 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 517
      removed outlier: 3.755A  pdb=" N   ASP C 511 " --> pdb=" O   THR C 507 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 51 through 60
      removed outlier: 3.533A  pdb=" N   ARG D  57 " --> pdb=" O   CYS D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 106
    Processing helix  chain 'D' and resid 123 through 140
    Processing helix  chain 'D' and resid 141 through 144
    Processing helix  chain 'D' and resid 195 through 200
    Processing helix  chain 'D' and resid 208 through 212
      removed outlier: 3.634A  pdb=" N   ARG D 212 " --> pdb=" O   SER D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 238
      removed outlier: 3.635A  pdb=" N   SER D 237 " --> pdb=" O   THR D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 329
      removed outlier: 3.716A  pdb=" N   LYS D 329 " --> pdb=" O   PHE D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 371
      removed outlier: 3.519A  pdb=" N   LEU D 349 " --> pdb=" O   GLY D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 375 through 398
      removed outlier: 3.552A  pdb=" N   LEU D 388 " --> pdb=" O   THR D 384 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE D 394 " --> pdb=" O   TRP D 390 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG D 395 " --> pdb=" O   VAL D 391 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR D 396 " --> pdb=" O   GLY D 392 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 406 through 411
    Processing helix  chain 'D' and resid 412 through 440
      removed outlier: 4.656A  pdb=" N   LYS D 416 " --> pdb=" O   ALA D 412 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   MET D 426 " --> pdb=" O   ALA D 422 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE D 427 " --> pdb=" O   CYS D 423 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 447
      removed outlier: 3.883A  pdb=" N   GLU D 447 " --> pdb=" O   ASP D 444 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 461
    Processing helix  chain 'D' and resid 464 through 472
      removed outlier: 4.408A  pdb=" N   ILE D 472 " --> pdb=" O   THR D 468 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 476 through 517
      removed outlier: 3.755A  pdb=" N   ASP D 511 " --> pdb=" O   THR D 507 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121
      removed outlier: 4.503A  pdb=" N   HIS A 226 " --> pdb=" O   GLY A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121
      removed outlier: 6.539A  pdb=" N   LEU A 218 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN A 220 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   HIS A 226 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLY A 160 " --> pdb=" O   HIS A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121
      removed outlier: 4.503A  pdb=" N   HIS B 226 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121
      removed outlier: 6.538A  pdb=" N   LEU B 218 " --> pdb=" O   TYR B 168 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   TYR B 168 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN B 220 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   HIS B 226 " --> pdb=" O   GLY B 160 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   GLY B 160 " --> pdb=" O   HIS B 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121
      removed outlier: 4.503A  pdb=" N   HIS C 226 " --> pdb=" O   GLY C 152 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121
      removed outlier: 6.539A  pdb=" N   LEU C 218 " --> pdb=" O   TYR C 168 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   TYR C 168 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN C 220 " --> pdb=" O   GLN C 166 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   HIS C 226 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLY C 160 " --> pdb=" O   HIS C 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121
      removed outlier: 4.503A  pdb=" N   HIS D 226 " --> pdb=" O   GLY D 152 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121
      removed outlier: 6.539A  pdb=" N   LEU D 218 " --> pdb=" O   TYR D 168 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   TYR D 168 " --> pdb=" O   LEU D 218 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN D 220 " --> pdb=" O   GLN D 166 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   HIS D 226 " --> pdb=" O   GLY D 160 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLY D 160 " --> pdb=" O   HIS D 226 " (cutoff:3.500A)

    1157 hydrogen bonds defined for protein.
    3375 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4577
        1.34 -     1.47: 3840
        1.47 -     1.60: 7011
        1.60 -     1.73: 0
        1.73 -     1.86: 136
  Bond restraints: 15564
  Sorted by residual:
  bond pdb=" C16 ZB4 A 601 "
       pdb=" N02 ZB4 A 601 "
    ideal  model  delta    sigma   weight residual
    1.468  1.358  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" C16 ZB4 D 601 "
       pdb=" N02 ZB4 D 601 "
    ideal  model  delta    sigma   weight residual
    1.468  1.359  0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" C16 ZB4 B 601 "
       pdb=" N02 ZB4 B 601 "
    ideal  model  delta    sigma   weight residual
    1.468  1.359  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" C16 ZB4 C 601 "
       pdb=" N02 ZB4 C 601 "
    ideal  model  delta    sigma   weight residual
    1.468  1.359  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" N01 ZB4 B 601 "
       pdb=" S01 ZB4 B 601 "
    ideal  model  delta    sigma   weight residual
    1.631  1.733 -0.102 2.00e-02 2.50e+03 2.61e+01
  ... (remaining 15559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 20762
        3.59 -     7.19: 226
        7.19 -    10.78: 24
       10.78 -    14.37: 8
       14.37 -    17.96: 8
  Bond angle restraints: 21028
  Sorted by residual:
  angle pdb=" C   LEU A 372 "
        pdb=" CA  LEU A 372 "
        pdb=" CB  LEU A 372 "
      ideal   model   delta    sigma   weight residual
     109.37   92.13   17.24 1.83e+00 2.99e-01 8.87e+01
  angle pdb=" C   LEU D 372 "
        pdb=" CA  LEU D 372 "
        pdb=" CB  LEU D 372 "
      ideal   model   delta    sigma   weight residual
     109.37   92.14   17.23 1.83e+00 2.99e-01 8.86e+01
  angle pdb=" C   LEU C 372 "
        pdb=" CA  LEU C 372 "
        pdb=" CB  LEU C 372 "
      ideal   model   delta    sigma   weight residual
     109.37   92.14   17.23 1.83e+00 2.99e-01 8.86e+01
  angle pdb=" C   LEU B 372 "
        pdb=" CA  LEU B 372 "
        pdb=" CB  LEU B 372 "
      ideal   model   delta    sigma   weight residual
     109.37   92.17   17.20 1.83e+00 2.99e-01 8.83e+01
  angle pdb=" C   ILE C 506 "
        pdb=" CA  ILE C 506 "
        pdb=" CB  ILE C 506 "
      ideal   model   delta    sigma   weight residual
     111.81  101.84    9.97 1.25e+00 6.40e-01 6.36e+01
  ... (remaining 21023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.31: 8928
       29.31 -    58.61: 256
       58.61 -    87.92: 28
       87.92 -   117.22: 16
      117.22 -   146.53: 4
  Dihedral angle restraints: 9232
    sinusoidal: 3800
      harmonic: 5432
  Sorted by residual:
  dihedral pdb=" C   LEU A 372 "
           pdb=" N   LEU A 372 "
           pdb=" CA  LEU A 372 "
           pdb=" CB  LEU A 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.58  -20.02     0      2.50e+00 1.60e-01 6.41e+01
  dihedral pdb=" C   LEU D 372 "
           pdb=" N   LEU D 372 "
           pdb=" CA  LEU D 372 "
           pdb=" CB  LEU D 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.58  -20.02     0      2.50e+00 1.60e-01 6.41e+01
  dihedral pdb=" C   LEU C 372 "
           pdb=" N   LEU C 372 "
           pdb=" CA  LEU C 372 "
           pdb=" CB  LEU C 372 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.61  -19.99     0      2.50e+00 1.60e-01 6.40e+01
  ... (remaining 9229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 2035
       0.075 -    0.149: 274
       0.149 -    0.224: 47
       0.224 -    0.298: 4
       0.298 -    0.373: 4
  Chirality restraints: 2364
  Sorted by residual:
  chirality pdb=" CA  LEU C 372 "
            pdb=" N   LEU C 372 "
            pdb=" C   LEU C 372 "
            pdb=" CB  LEU C 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  LEU D 372 "
            pdb=" N   LEU D 372 "
            pdb=" C   LEU D 372 "
            pdb=" CB  LEU D 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  LEU A 372 "
            pdb=" N   LEU A 372 "
            pdb=" C   LEU A 372 "
            pdb=" CB  LEU A 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.47e+00
  ... (remaining 2361 not shown)

  Planarity restraints: 2572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 460 "    0.027 2.00e-02 2.50e+03   5.05e-02 2.55e+01
        pdb=" C   VAL B 460 "   -0.087 2.00e-02 2.50e+03
        pdb=" O   VAL B 460 "    0.031 2.00e-02 2.50e+03
        pdb=" N   ASN B 461 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 460 "    0.027 2.00e-02 2.50e+03   5.03e-02 2.53e+01
        pdb=" C   VAL A 460 "   -0.087 2.00e-02 2.50e+03
        pdb=" O   VAL A 460 "    0.031 2.00e-02 2.50e+03
        pdb=" N   ASN A 461 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 460 "   -0.027 2.00e-02 2.50e+03   5.02e-02 2.52e+01
        pdb=" C   VAL C 460 "    0.087 2.00e-02 2.50e+03
        pdb=" O   VAL C 460 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ASN C 461 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 2569 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 683
        2.72 -     3.27: 15500
        3.27 -     3.81: 24760
        3.81 -     4.36: 31064
        4.36 -     4.90: 52649
  Nonbonded interactions: 124656
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS D 167 "
            pdb=" O   LEU D 213 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" NE2 HIS B 167 "
            pdb=" O   LEU B 213 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" NE2 HIS A 167 "
            pdb=" O   LEU A 213 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" NE2 HIS C 167 "
            pdb=" O   LEU C 213 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" OH  TYR C 428 "
            pdb=" O   ALA C 453 "
     model   vdw
     2.220 3.040
  ... (remaining 124651 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             2.080
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.540
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
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      :  0.008   0.110  15572  Z= 0.467
  Angle     :  1.019  17.965  21044  Z= 0.671
  Chirality :  0.057   0.373   2364
  Planarity :  0.005   0.050   2572
  Dihedral  : 14.895 146.531   5696
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.18 %
    Favored  : 92.11 %
  Cbeta Deviations :  0.46 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.20), residues: 1804
  helix:  1.19 (0.15), residues: 1148
  sheet:  1.53 (0.37), residues: 220
  loop : -1.28 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  59 
 TYR   0.015   0.001   TYR A 486 
 PHE   0.018   0.002   PHE D 502 
 TRP   0.014   0.002   TRP D  64 
 HIS   0.003   0.001   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 (15564)
  covalent geometry    : angle       1.01887 (21028)
  SS BOND              : bond        0.00134 (    8)
  SS BOND              : angle       0.37160 (   16)
  hydrogen bonds       : bond        0.17043 ( 1061)
  hydrogen bonds       : angle       7.05952 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.4518 (pmm) cc_final: 0.4159 (tpt)
REVERT: A   95 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7814 (mt-10)
REVERT: A  187 GLU cc_start: 0.7648 (pt0) cc_final: 0.7306 (pt0)
REVERT: A  196 GLN cc_start: 0.7883 (mp10) cc_final: 0.7045 (mp10)
REVERT: A  368 LYS cc_start: 0.8426 (tppp) cc_final: 0.7926 (tptp)
REVERT: A  464 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8134 (t0)
REVERT: B   36 MET cc_start: 0.4449 (pmm) cc_final: 0.4012 (tpt)
REVERT: B   95 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7783 (mt-10)
REVERT: B  158 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.6594 (ptm160)
REVERT: B  187 GLU cc_start: 0.7708 (pt0) cc_final: 0.7376 (pt0)
REVERT: B  196 GLN cc_start: 0.7894 (mp10) cc_final: 0.7097 (mp10)
REVERT: B  278 ASN cc_start: 0.6990 (m-40) cc_final: 0.6661 (m110)
REVERT: B  368 LYS cc_start: 0.8380 (tppp) cc_final: 0.7906 (tptp)
REVERT: B  464 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (t0)
REVERT: C   36 MET cc_start: 0.4493 (pmm) cc_final: 0.4141 (tpt)
REVERT: C   95 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7790 (mt-10)
REVERT: C  158 ARG cc_start: 0.7341 (tpp-160) cc_final: 0.6647 (ptm160)
REVERT: C  187 GLU cc_start: 0.7728 (pt0) cc_final: 0.7388 (pt0)
REVERT: C  196 GLN cc_start: 0.7864 (mp10) cc_final: 0.7115 (mp10)
REVERT: C  278 ASN cc_start: 0.6747 (m-40) cc_final: 0.6410 (m110)
REVERT: C  368 LYS cc_start: 0.8388 (tppp) cc_final: 0.7905 (tptp)
REVERT: C  464 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8106 (t0)
REVERT: D   36 MET cc_start: 0.4555 (pmm) cc_final: 0.4205 (tpt)
REVERT: D   95 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7752 (mt-10)
REVERT: D  185 ASP cc_start: 0.7817 (t0) cc_final: 0.7576 (p0)
REVERT: D  187 GLU cc_start: 0.7731 (pt0) cc_final: 0.7437 (pt0)
REVERT: D  196 GLN cc_start: 0.7904 (mp10) cc_final: 0.7109 (mp10)
REVERT: D  278 ASN cc_start: 0.6713 (m-40) cc_final: 0.6340 (m110)
REVERT: D  368 LYS cc_start: 0.8338 (tppp) cc_final: 0.7861 (tptp)
REVERT: D  464 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8164 (t0)
  outliers start: 12
  outliers final: 0
  residues processed: 203
  average time/residue: 0.5903
  time to fit residues: 132.1010
Evaluate side-chains
  164 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 160
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ASP
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain C residue  464 ASP
Chi-restraints excluded: chain D residue  464 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 181 ASN
A 471 GLN
B  69 GLN
B 181 ASN
B 471 GLN
C  69 GLN
C 181 ASN
C 471 GLN
D  69 GLN
D 471 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.158648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111764 restraints weight = 17809.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.13
r_work: 0.3184 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  15572  Z= 0.189
  Angle     :  0.554   5.646  21044  Z= 0.302
  Chirality :  0.041   0.149   2364
  Planarity :  0.004   0.039   2572
  Dihedral  : 12.019 120.864   2104
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  :  9.21 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.20), residues: 1804
  helix:  2.37 (0.15), residues: 1112
  sheet:  1.97 (0.36), residues: 200
  loop : -1.38 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  59 
 TYR   0.016   0.001   TYR C 264 
 PHE   0.016   0.002   PHE C 494 
 TRP   0.012   0.001   TRP C 390 
 HIS   0.002   0.001   HIS D 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (15564)
  covalent geometry    : angle       0.55371 (21028)
  SS BOND              : bond        0.00136 (    8)
  SS BOND              : angle       0.67204 (   16)
  hydrogen bonds       : bond        0.05615 ( 1061)
  hydrogen bonds       : angle       4.62376 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 176
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A   36 MET cc_start: 0.4734 (pmm) cc_final: 0.4459 (tpt)
REVERT: A   95 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7704 (mt-10)
REVERT: A  158 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.6683 (ptm160)
REVERT: A  185 ASP cc_start: 0.7888 (t0) cc_final: 0.7640 (p0)
REVERT: A  187 GLU cc_start: 0.7841 (pt0) cc_final: 0.7602 (pt0)
REVERT: A  194 ASP cc_start: 0.7858 (t0) cc_final: 0.6943 (t0)
REVERT: A  196 GLN cc_start: 0.7342 (mp10) cc_final: 0.6801 (mp10)
REVERT: A  254 ASN cc_start: 0.7963 (p0) cc_final: 0.7652 (p0)
REVERT: A  368 LYS cc_start: 0.8405 (tppp) cc_final: 0.7888 (tptp)
REVERT: B   36 MET cc_start: 0.4493 (pmm) cc_final: 0.4261 (tpt)
REVERT: B   95 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7697 (mt-10)
REVERT: B  157 ASN cc_start: 0.7838 (t0) cc_final: 0.7602 (t0)
REVERT: B  158 ARG cc_start: 0.7421 (tpp-160) cc_final: 0.6686 (ptm160)
REVERT: B  185 ASP cc_start: 0.7893 (t0) cc_final: 0.7656 (p0)
REVERT: B  187 GLU cc_start: 0.7844 (pt0) cc_final: 0.7605 (pt0)
REVERT: B  194 ASP cc_start: 0.7829 (t0) cc_final: 0.6971 (t0)
REVERT: B  196 GLN cc_start: 0.7352 (mp10) cc_final: 0.6846 (mp10)
REVERT: B  278 ASN cc_start: 0.7189 (m-40) cc_final: 0.6880 (m110)
REVERT: B  368 LYS cc_start: 0.8337 (tppp) cc_final: 0.7838 (tptp)
REVERT: C   48 TYR cc_start: 0.7767 (t80) cc_final: 0.7157 (t80)
REVERT: C   95 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7689 (mt-10)
REVERT: C  158 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.6688 (ptm160)
REVERT: C  185 ASP cc_start: 0.7887 (t0) cc_final: 0.7655 (p0)
REVERT: C  187 GLU cc_start: 0.7849 (pt0) cc_final: 0.7607 (pt0)
REVERT: C  194 ASP cc_start: 0.7860 (t0) cc_final: 0.6997 (t0)
REVERT: C  196 GLN cc_start: 0.7333 (mp10) cc_final: 0.6822 (mp10)
REVERT: C  278 ASN cc_start: 0.7128 (m-40) cc_final: 0.6821 (m110)
REVERT: C  368 LYS cc_start: 0.8362 (tppp) cc_final: 0.7861 (tptp)
REVERT: D   36 MET cc_start: 0.4566 (pmm) cc_final: 0.4292 (tpt)
REVERT: D   48 TYR cc_start: 0.7591 (t80) cc_final: 0.7045 (t80)
REVERT: D   73 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7911 (mm)
REVERT: D   95 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7689 (mt-10)
REVERT: D  157 ASN cc_start: 0.7855 (t0) cc_final: 0.7619 (t0)
REVERT: D  158 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.6696 (ptm160)
REVERT: D  187 GLU cc_start: 0.7835 (pt0) cc_final: 0.7586 (pt0)
REVERT: D  194 ASP cc_start: 0.7851 (t0) cc_final: 0.7007 (t0)
REVERT: D  196 GLN cc_start: 0.7413 (mp10) cc_final: 0.6898 (mp10)
REVERT: D  278 ASN cc_start: 0.7131 (m-40) cc_final: 0.6836 (m110)
REVERT: D  368 LYS cc_start: 0.8305 (tppp) cc_final: 0.7796 (tptp)
  outliers start: 47
  outliers final: 23
  residues processed: 206
  average time/residue: 0.5450
  time to fit residues: 124.9991
Evaluate side-chains
  193 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  471 GLN
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  471 GLN
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  471 GLN
Chi-restraints excluded: chain D residue  497 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 164 optimal weight:    0.9990
   chunk 118 optimal weight:    9.9990
   chunk 167 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 140 optimal weight:    0.8980
   chunk 169 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 471 GLN
B 181 ASN
B 471 GLN
C 181 ASN
C 471 GLN
D 181 ASN
D 471 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.153342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.103632 restraints weight = 17208.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.13
r_work: 0.3045 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
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      :  0.003   0.023  15572  Z= 0.146
  Angle     :  0.492   5.708  21044  Z= 0.266
  Chirality :  0.039   0.136   2364
  Planarity :  0.003   0.039   2572
  Dihedral  : 11.407 113.984   2096
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.36 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.20), residues: 1804
  helix:  2.72 (0.15), residues: 1120
  sheet:  1.69 (0.34), residues: 220
  loop : -1.11 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 317 
 TYR   0.015   0.001   TYR B 264 
 PHE   0.015   0.001   PHE C 494 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS D 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15564)
  covalent geometry    : angle       0.49202 (21028)
  SS BOND              : bond        0.00065 (    8)
  SS BOND              : angle       0.58900 (   16)
  hydrogen bonds       : bond        0.05053 ( 1061)
  hydrogen bonds       : angle       4.32147 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.4800 (pmm) cc_final: 0.4500 (tpt)
REVERT: A   48 TYR cc_start: 0.7683 (t80) cc_final: 0.7197 (t80)
REVERT: A   50 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7009 (ptm)
REVERT: A   54 GLU cc_start: 0.7776 (tt0) cc_final: 0.7473 (tm-30)
REVERT: A   95 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7850 (mt-10)
REVERT: A  157 ASN cc_start: 0.7914 (t0) cc_final: 0.7630 (t0)
REVERT: A  158 ARG cc_start: 0.7577 (tpp-160) cc_final: 0.6753 (ptm160)
REVERT: A  194 ASP cc_start: 0.7969 (t0) cc_final: 0.6997 (t0)
REVERT: A  196 GLN cc_start: 0.7371 (mp10) cc_final: 0.6834 (mp10)
REVERT: A  368 LYS cc_start: 0.8455 (tppp) cc_final: 0.7935 (tptp)
REVERT: B   48 TYR cc_start: 0.7736 (t80) cc_final: 0.7260 (t80)
REVERT: B   50 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7115 (ptm)
REVERT: B   54 GLU cc_start: 0.7819 (tt0) cc_final: 0.7444 (tm-30)
REVERT: B   95 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7849 (mt-10)
REVERT: B  158 ARG cc_start: 0.7515 (tpp-160) cc_final: 0.6791 (ptm160)
REVERT: B  194 ASP cc_start: 0.7936 (t0) cc_final: 0.7002 (t0)
REVERT: B  196 GLN cc_start: 0.7352 (mp10) cc_final: 0.6833 (mp10)
REVERT: B  278 ASN cc_start: 0.7312 (m-40) cc_final: 0.7073 (m110)
REVERT: B  368 LYS cc_start: 0.8423 (tppp) cc_final: 0.7902 (tptp)
REVERT: C   48 TYR cc_start: 0.7676 (t80) cc_final: 0.7082 (t80)
REVERT: C   54 GLU cc_start: 0.7848 (tt0) cc_final: 0.7492 (tm-30)
REVERT: C   95 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7861 (mt-10)
REVERT: C  158 ARG cc_start: 0.7492 (tpp-160) cc_final: 0.6851 (ptm160)
REVERT: C  194 ASP cc_start: 0.7984 (t0) cc_final: 0.7598 (t0)
REVERT: C  278 ASN cc_start: 0.7226 (m-40) cc_final: 0.6973 (m110)
REVERT: C  368 LYS cc_start: 0.8452 (tppp) cc_final: 0.7936 (tptp)
REVERT: D   36 MET cc_start: 0.4468 (pmm) cc_final: 0.4240 (tpt)
REVERT: D   48 TYR cc_start: 0.7582 (t80) cc_final: 0.6993 (t80)
REVERT: D   95 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7843 (mt-10)
REVERT: D  158 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.6744 (ptm160)
REVERT: D  169 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7226 (mtpp)
REVERT: D  187 GLU cc_start: 0.7841 (pt0) cc_final: 0.7593 (pt0)
REVERT: D  194 ASP cc_start: 0.7961 (t0) cc_final: 0.7065 (t0)
REVERT: D  196 GLN cc_start: 0.7376 (mp10) cc_final: 0.6862 (mp10)
REVERT: D  278 ASN cc_start: 0.7293 (m-40) cc_final: 0.7051 (m110)
REVERT: D  368 LYS cc_start: 0.8368 (tppp) cc_final: 0.7860 (tptp)
  outliers start: 39
  outliers final: 19
  residues processed: 187
  average time/residue: 0.6081
  time to fit residues: 125.6107
Evaluate side-chains
  183 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  471 GLN
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  471 GLN
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  471 GLN
Chi-restraints excluded: chain D residue  497 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   chunk 148 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 142 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 471 GLN
B 181 ASN
B 471 GLN
C 181 ASN
C 471 GLN
D 181 ASN
D 471 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.151078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.100450 restraints weight = 17295.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.23
r_work: 0.2996 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  15572  Z= 0.214
  Angle     :  0.531   5.097  21044  Z= 0.289
  Chirality :  0.041   0.149   2364
  Planarity :  0.003   0.039   2572
  Dihedral  : 11.434 113.529   2096
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 10.65 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.20), residues: 1804
  helix:  2.67 (0.14), residues: 1120
  sheet:  1.58 (0.34), residues: 220
  loop : -1.01 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 317 
 TYR   0.013   0.002   TYR B 375 
 PHE   0.017   0.002   PHE C 494 
 TRP   0.010   0.001   TRP D 390 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (15564)
  covalent geometry    : angle       0.53062 (21028)
  SS BOND              : bond        0.00200 (    8)
  SS BOND              : angle       0.63454 (   16)
  hydrogen bonds       : bond        0.05588 ( 1061)
  hydrogen bonds       : angle       4.36143 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 174
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.4656 (pmm) cc_final: 0.4423 (tpt)
REVERT: A   50 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7013 (ptm)
REVERT: A   54 GLU cc_start: 0.7881 (tt0) cc_final: 0.7434 (tm-30)
REVERT: A   95 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7874 (mt-10)
REVERT: A  157 ASN cc_start: 0.7999 (t0) cc_final: 0.7746 (t0)
REVERT: A  158 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.6622 (ptm160)
REVERT: A  169 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7242 (mtpp)
REVERT: A  194 ASP cc_start: 0.7933 (t0) cc_final: 0.7059 (t0)
REVERT: A  196 GLN cc_start: 0.7350 (mp10) cc_final: 0.6879 (mp10)
REVERT: A  368 LYS cc_start: 0.8427 (tppp) cc_final: 0.7914 (tptp)
REVERT: B   50 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7016 (ptm)
REVERT: B   54 GLU cc_start: 0.7840 (tt0) cc_final: 0.7486 (tm-30)
REVERT: B   95 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7869 (mt-10)
REVERT: B  169 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7239 (mtpp)
REVERT: B  194 ASP cc_start: 0.7919 (t0) cc_final: 0.7097 (t0)
REVERT: B  196 GLN cc_start: 0.7312 (mp10) cc_final: 0.6867 (mp10)
REVERT: B  278 ASN cc_start: 0.7314 (m-40) cc_final: 0.7073 (m110)
REVERT: B  368 LYS cc_start: 0.8399 (tppp) cc_final: 0.7889 (tptp)
REVERT: C   95 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7858 (mt-10)
REVERT: C  158 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.6674 (ptm160)
REVERT: C  169 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7217 (mtpp)
REVERT: C  194 ASP cc_start: 0.7925 (t0) cc_final: 0.7071 (t0)
REVERT: C  196 GLN cc_start: 0.7319 (mp10) cc_final: 0.6876 (mp10)
REVERT: C  278 ASN cc_start: 0.7294 (m-40) cc_final: 0.7050 (m110)
REVERT: C  368 LYS cc_start: 0.8426 (tppp) cc_final: 0.7906 (tptp)
REVERT: D   36 MET cc_start: 0.4411 (pmm) cc_final: 0.4204 (tpt)
REVERT: D   54 GLU cc_start: 0.7873 (tt0) cc_final: 0.7415 (tm-30)
REVERT: D   95 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7850 (mt-10)
REVERT: D  158 ARG cc_start: 0.7553 (tpp-160) cc_final: 0.6644 (ptm160)
REVERT: D  187 GLU cc_start: 0.7850 (pt0) cc_final: 0.7631 (pt0)
REVERT: D  194 ASP cc_start: 0.7916 (t0) cc_final: 0.7102 (t0)
REVERT: D  196 GLN cc_start: 0.7351 (mp10) cc_final: 0.6930 (mp10)
REVERT: D  278 ASN cc_start: 0.7316 (m-40) cc_final: 0.7064 (m110)
REVERT: D  368 LYS cc_start: 0.8381 (tppp) cc_final: 0.7862 (tptp)
  outliers start: 60
  outliers final: 35
  residues processed: 209
  average time/residue: 0.5996
  time to fit residues: 138.9904
Evaluate side-chains
  201 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  471 GLN
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  471 GLN
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain C residue  512 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain D residue  471 GLN
Chi-restraints excluded: chain D residue  497 MET
Chi-restraints excluded: chain D residue  512 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 147 optimal weight:    2.9990
   chunk 164 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 168 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 148 optimal weight:    0.9980
   chunk 176 optimal weight:    0.2980
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 448 ASN
A 471 GLN
B 181 ASN
B 448 ASN
B 471 GLN
C 181 ASN
C 448 ASN
C 471 GLN
D 181 ASN
D 448 ASN
D 471 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.162175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.114440 restraints weight = 17873.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.18
r_work: 0.3250 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15572  Z= 0.119
  Angle     :  0.465   5.872  21044  Z= 0.252
  Chirality :  0.038   0.139   2364
  Planarity :  0.003   0.043   2572
  Dihedral  : 11.010 106.066   2096
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.20 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.20), residues: 1804
  helix:  2.98 (0.15), residues: 1116
  sheet:  1.64 (0.33), residues: 220
  loop : -0.95 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  59 
 TYR   0.015   0.001   TYR B 264 
 PHE   0.016   0.001   PHE B 400 
 TRP   0.009   0.001   TRP D  64 
 HIS   0.002   0.001   HIS D 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (15564)
  covalent geometry    : angle       0.46476 (21028)
  SS BOND              : bond        0.00098 (    8)
  SS BOND              : angle       0.33194 (   16)
  hydrogen bonds       : bond        0.04590 ( 1061)
  hydrogen bonds       : angle       4.12758 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.4732 (pmm) cc_final: 0.4489 (tpt)
REVERT: A   50 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7009 (ptm)
REVERT: A   54 GLU cc_start: 0.7877 (tt0) cc_final: 0.7430 (tm-30)
REVERT: A   95 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7641 (mt-10)
REVERT: A  157 ASN cc_start: 0.8113 (t0) cc_final: 0.7850 (t0)
REVERT: A  158 ARG cc_start: 0.7605 (tpp-160) cc_final: 0.6683 (ptm160)
REVERT: A  169 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7095 (mtpp)
REVERT: A  194 ASP cc_start: 0.7811 (t0) cc_final: 0.7437 (t0)
REVERT: A  368 LYS cc_start: 0.8267 (tppp) cc_final: 0.7752 (tptp)
REVERT: B   50 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7074 (ptm)
REVERT: B   54 GLU cc_start: 0.7846 (tt0) cc_final: 0.7477 (tm-30)
REVERT: B   95 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7622 (mt-10)
REVERT: B  158 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.6716 (ptm160)
REVERT: B  169 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7125 (mtpp)
REVERT: B  194 ASP cc_start: 0.7824 (t0) cc_final: 0.7438 (t0)
REVERT: B  368 LYS cc_start: 0.8264 (tppp) cc_final: 0.7736 (tptp)
REVERT: C   36 MET cc_start: 0.4285 (tpt) cc_final: 0.4057 (tpt)
REVERT: C   95 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7622 (mt-10)
REVERT: C  158 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.6738 (ptm160)
REVERT: C  169 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7102 (mtpp)
REVERT: C  194 ASP cc_start: 0.7792 (t0) cc_final: 0.7406 (t0)
REVERT: C  278 ASN cc_start: 0.7313 (m-40) cc_final: 0.7062 (m110)
REVERT: C  368 LYS cc_start: 0.8270 (tppp) cc_final: 0.7732 (tptp)
REVERT: D   95 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7595 (mt-10)
REVERT: D  158 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.6648 (ptm160)
REVERT: D  194 ASP cc_start: 0.7804 (t0) cc_final: 0.7424 (t0)
REVERT: D  278 ASN cc_start: 0.7312 (m-40) cc_final: 0.7052 (m110)
REVERT: D  368 LYS cc_start: 0.8274 (tppp) cc_final: 0.7747 (tptp)
  outliers start: 34
  outliers final: 20
  residues processed: 188
  average time/residue: 0.5342
  time to fit residues: 112.0840
Evaluate side-chains
  179 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  471 GLN
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  471 GLN
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  471 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 173 optimal weight:    0.9980
   chunk 155 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 156 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 141 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 471 GLN
B 181 ASN
B 471 GLN
C 181 ASN
C 471 GLN
D 471 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.154852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104349 restraints weight = 17155.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.16
r_work: 0.3065 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  15572  Z= 0.137
  Angle     :  0.467   6.166  21044  Z= 0.253
  Chirality :  0.038   0.139   2364
  Planarity :  0.003   0.041   2572
  Dihedral  : 10.859 103.001   2096
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 12.44 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.86 (0.20), residues: 1804
  helix:  3.00 (0.15), residues: 1116
  sheet:  1.67 (0.34), residues: 220
  loop : -0.92 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  59 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.015   0.001   PHE A 400 
 TRP   0.008   0.001   TRP C  64 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (15564)
  covalent geometry    : angle       0.46736 (21028)
  SS BOND              : bond        0.00123 (    8)
  SS BOND              : angle       0.35804 (   16)
  hydrogen bonds       : bond        0.04686 ( 1061)
  hydrogen bonds       : angle       4.09547 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 163
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7049 (ptm)
REVERT: A   54 GLU cc_start: 0.7926 (tt0) cc_final: 0.7458 (tm-30)
REVERT: A   95 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7765 (mt-10)
REVERT: A  158 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.6758 (ptm160)
REVERT: A  169 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7241 (mtpp)
REVERT: A  194 ASP cc_start: 0.8002 (t0) cc_final: 0.7088 (t0)
REVERT: A  196 GLN cc_start: 0.7263 (mp10) cc_final: 0.6890 (mp10)
REVERT: A  368 LYS cc_start: 0.8384 (tppp) cc_final: 0.7882 (tptp)
REVERT: B   50 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7110 (ptm)
REVERT: B   54 GLU cc_start: 0.7817 (tt0) cc_final: 0.7424 (tm-30)
REVERT: B   95 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7785 (mt-10)
REVERT: B  158 ARG cc_start: 0.7646 (tpp-160) cc_final: 0.6798 (ptm160)
REVERT: B  169 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7257 (mtpp)
REVERT: B  194 ASP cc_start: 0.8002 (t0) cc_final: 0.7641 (t0)
REVERT: B  278 ASN cc_start: 0.7395 (m-40) cc_final: 0.7138 (m110)
REVERT: B  368 LYS cc_start: 0.8421 (tppp) cc_final: 0.7907 (tptp)
REVERT: C   36 MET cc_start: 0.4365 (tpt) cc_final: 0.4076 (tpt)
REVERT: C   95 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7774 (mt-10)
REVERT: C  158 ARG cc_start: 0.7487 (tpp-160) cc_final: 0.6815 (ptm160)
REVERT: C  169 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7248 (mtpp)
REVERT: C  194 ASP cc_start: 0.7999 (t0) cc_final: 0.7636 (t0)
REVERT: C  278 ASN cc_start: 0.7365 (m-40) cc_final: 0.7119 (m110)
REVERT: C  368 LYS cc_start: 0.8412 (tppp) cc_final: 0.7898 (tptp)
REVERT: D   95 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7784 (mt-10)
REVERT: D  158 ARG cc_start: 0.7581 (tpp-160) cc_final: 0.6812 (ptm160)
REVERT: D  194 ASP cc_start: 0.7983 (t0) cc_final: 0.7650 (t0)
REVERT: D  278 ASN cc_start: 0.7388 (m-40) cc_final: 0.7130 (m110)
REVERT: D  368 LYS cc_start: 0.8357 (tppp) cc_final: 0.7834 (tptp)
  outliers start: 49
  outliers final: 35
  residues processed: 187
  average time/residue: 0.5472
  time to fit residues: 114.3319
Evaluate side-chains
  196 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 159
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  119 CYS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  471 GLN
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  119 CYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  471 GLN
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  119 CYS
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  471 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 173 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 116 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 ASN
** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.103825 restraints weight = 16777.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.20
r_work: 0.3049 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15572  Z= 0.140
  Angle     :  0.478   8.912  21044  Z= 0.258
  Chirality :  0.038   0.139   2364
  Planarity :  0.003   0.041   2572
  Dihedral  : 10.689 100.300   2096
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.62 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.20), residues: 1804
  helix:  3.02 (0.14), residues: 1116
  sheet:  1.64 (0.34), residues: 220
  loop : -0.90 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  59 
 TYR   0.014   0.001   TYR D 486 
 PHE   0.014   0.001   PHE C 494 
 TRP   0.008   0.001   TRP C  64 
 HIS   0.002   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (15564)
  covalent geometry    : angle       0.47815 (21028)
  SS BOND              : bond        0.00120 (    8)
  SS BOND              : angle       0.34784 (   16)
  hydrogen bonds       : bond        0.04669 ( 1061)
  hydrogen bonds       : angle       4.08338 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 167
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7058 (ptm)
REVERT: A   54 GLU cc_start: 0.7886 (tt0) cc_final: 0.7420 (tm-30)
REVERT: A   95 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7763 (mt-10)
REVERT: A  158 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.6758 (ptm160)
REVERT: A  169 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7205 (mtpp)
REVERT: A  194 ASP cc_start: 0.7972 (t0) cc_final: 0.7007 (t0)
REVERT: A  196 GLN cc_start: 0.7212 (mp10) cc_final: 0.6832 (mp10)
REVERT: A  368 LYS cc_start: 0.8357 (tppp) cc_final: 0.7850 (tptp)
REVERT: A  471 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8216 (tt0)
REVERT: B   50 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7006 (ptm)
REVERT: B   54 GLU cc_start: 0.7848 (tt0) cc_final: 0.7474 (tm-30)
REVERT: B   95 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7746 (mt-10)
REVERT: B  158 ARG cc_start: 0.7569 (tpp-160) cc_final: 0.6726 (ptm160)
REVERT: B  169 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7195 (mtpp)
REVERT: B  194 ASP cc_start: 0.7959 (t0) cc_final: 0.7227 (t0)
REVERT: B  196 GLN cc_start: 0.7200 (mp10) cc_final: 0.6900 (mp10)
REVERT: B  278 ASN cc_start: 0.7370 (m-40) cc_final: 0.7103 (m110)
REVERT: B  368 LYS cc_start: 0.8374 (tppp) cc_final: 0.7856 (tptp)
REVERT: B  471 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8231 (tt0)
REVERT: B  502 PHE cc_start: 0.8246 (t80) cc_final: 0.7738 (t80)
REVERT: C   36 MET cc_start: 0.4197 (tpt) cc_final: 0.3940 (tpt)
REVERT: C   95 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7754 (mt-10)
REVERT: C  158 ARG cc_start: 0.7389 (tpp-160) cc_final: 0.6741 (ptm160)
REVERT: C  169 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7208 (mtpp)
REVERT: C  194 ASP cc_start: 0.7975 (t0) cc_final: 0.7612 (t0)
REVERT: C  278 ASN cc_start: 0.7336 (m-40) cc_final: 0.7074 (m110)
REVERT: C  368 LYS cc_start: 0.8370 (tppp) cc_final: 0.7852 (tptp)
REVERT: C  471 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8230 (tt0)
REVERT: D   95 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7755 (mt-10)
REVERT: D  158 ARG cc_start: 0.7488 (tpp-160) cc_final: 0.6699 (ptm160)
REVERT: D  194 ASP cc_start: 0.7967 (t0) cc_final: 0.7608 (t0)
REVERT: D  278 ASN cc_start: 0.7344 (m-40) cc_final: 0.7083 (m110)
REVERT: D  368 LYS cc_start: 0.8324 (tppp) cc_final: 0.7797 (tptp)
REVERT: D  471 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8237 (tt0)
  outliers start: 47
  outliers final: 32
  residues processed: 189
  average time/residue: 0.5428
  time to fit residues: 114.6926
Evaluate side-chains
  199 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 161
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  119 CYS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  471 GLN
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  119 CYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  471 GLN
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  119 CYS
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  471 GLN
Chi-restraints excluded: chain D residue  497 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 130 optimal weight:    0.9980
   chunk 118 optimal weight:    4.9990
   chunk 153 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9980
   chunk 167 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 181 ASN
A 461 ASN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
B 461 ASN
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 ASN
C 461 ASN
** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 461 ASN
** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.156493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105561 restraints weight = 16974.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.21
r_work: 0.3073 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15572  Z= 0.119
  Angle     :  0.465   9.310  21044  Z= 0.250
  Chirality :  0.038   0.140   2364
  Planarity :  0.003   0.042   2572
  Dihedral  :  9.993  91.477   2096
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.82 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.99 (0.20), residues: 1804
  helix:  3.09 (0.15), residues: 1120
  sheet:  1.64 (0.34), residues: 220
  loop : -0.81 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  59 
 TYR   0.017   0.001   TYR D  48 
 PHE   0.012   0.001   PHE D 494 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (15564)
  covalent geometry    : angle       0.46470 (21028)
  SS BOND              : bond        0.00113 (    8)
  SS BOND              : angle       0.30835 (   16)
  hydrogen bonds       : bond        0.04298 ( 1061)
  hydrogen bonds       : angle       3.99274 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 176
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7407 (mm-30)
REVERT: A  159 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7700 (mt)
REVERT: A  169 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7220 (mtpp)
REVERT: A  194 ASP cc_start: 0.8001 (t0) cc_final: 0.6995 (t0)
REVERT: A  196 GLN cc_start: 0.7284 (mp10) cc_final: 0.6860 (mp10)
REVERT: A  309 THR cc_start: 0.8189 (m) cc_final: 0.7822 (m)
REVERT: A  368 LYS cc_start: 0.8335 (tppp) cc_final: 0.7825 (tptp)
REVERT: B   50 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7040 (ptm)
REVERT: B   54 GLU cc_start: 0.7837 (tt0) cc_final: 0.7447 (tm-30)
REVERT: B   95 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: B  158 ARG cc_start: 0.7568 (tpp-160) cc_final: 0.6797 (ptm160)
REVERT: B  169 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7200 (mtpp)
REVERT: B  194 ASP cc_start: 0.7982 (t0) cc_final: 0.7616 (t0)
REVERT: B  309 THR cc_start: 0.8219 (m) cc_final: 0.7866 (m)
REVERT: B  368 LYS cc_start: 0.8371 (tppp) cc_final: 0.7844 (tptp)
REVERT: C   36 MET cc_start: 0.4366 (tpt) cc_final: 0.4133 (tpt)
REVERT: C   95 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: C  169 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7239 (mtpp)
REVERT: C  194 ASP cc_start: 0.8004 (t0) cc_final: 0.7687 (t0)
REVERT: C  278 ASN cc_start: 0.7350 (m-40) cc_final: 0.7093 (m110)
REVERT: C  309 THR cc_start: 0.8230 (m) cc_final: 0.7873 (m)
REVERT: C  368 LYS cc_start: 0.8359 (tppp) cc_final: 0.7826 (tptp)
REVERT: D   95 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7399 (mm-30)
REVERT: D  158 ARG cc_start: 0.7519 (tpp-160) cc_final: 0.6705 (ptm160)
REVERT: D  169 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7646 (mtmm)
REVERT: D  194 ASP cc_start: 0.8007 (t0) cc_final: 0.7644 (t0)
REVERT: D  278 ASN cc_start: 0.7379 (m-40) cc_final: 0.7125 (m110)
REVERT: D  309 THR cc_start: 0.8231 (m) cc_final: 0.7871 (m)
REVERT: D  368 LYS cc_start: 0.8296 (tppp) cc_final: 0.7752 (tptp)
  outliers start: 42
  outliers final: 32
  residues processed: 197
  average time/residue: 0.5112
  time to fit residues: 113.2851
Evaluate side-chains
  200 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  119 CYS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  207 ASN
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain C residue  119 CYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  207 ASN
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  119 CYS
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  207 ASN
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain D residue  497 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 175 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 149 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 177 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 181 ASN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 ASN
** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.155876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.104788 restraints weight = 16849.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.20
r_work: 0.3065 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15572  Z= 0.128
  Angle     :  0.482  10.059  21044  Z= 0.259
  Chirality :  0.038   0.134   2364
  Planarity :  0.003   0.043   2572
  Dihedral  :  9.499  84.394   2096
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.23 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.01 (0.20), residues: 1804
  helix:  3.08 (0.15), residues: 1120
  sheet:  1.71 (0.34), residues: 220
  loop : -0.77 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  59 
 TYR   0.014   0.001   TYR B 486 
 PHE   0.013   0.001   PHE C 494 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (15564)
  covalent geometry    : angle       0.48177 (21028)
  SS BOND              : bond        0.00117 (    8)
  SS BOND              : angle       0.30446 (   16)
  hydrogen bonds       : bond        0.04410 ( 1061)
  hydrogen bonds       : angle       4.00751 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 164
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: A  158 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.6794 (ptm160)
REVERT: A  169 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7282 (mtpp)
REVERT: A  194 ASP cc_start: 0.8083 (t0) cc_final: 0.7748 (t0)
REVERT: A  309 THR cc_start: 0.8223 (m) cc_final: 0.7857 (m)
REVERT: A  368 LYS cc_start: 0.8341 (tppp) cc_final: 0.7822 (tptp)
REVERT: A  508 ASP cc_start: 0.8165 (t0) cc_final: 0.7867 (m-30)
REVERT: B   50 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6995 (ptm)
REVERT: B   54 GLU cc_start: 0.7879 (tt0) cc_final: 0.7455 (tm-30)
REVERT: B   95 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7424 (mm-30)
REVERT: B  157 ASN cc_start: 0.8162 (t0) cc_final: 0.7956 (t0)
REVERT: B  158 ARG cc_start: 0.7518 (tpp-160) cc_final: 0.6664 (ptm160)
REVERT: B  169 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7216 (mtpp)
REVERT: B  194 ASP cc_start: 0.7999 (t0) cc_final: 0.7634 (t0)
REVERT: B  278 ASN cc_start: 0.7406 (m-40) cc_final: 0.7138 (m110)
REVERT: B  309 THR cc_start: 0.8223 (m) cc_final: 0.7869 (m)
REVERT: B  368 LYS cc_start: 0.8378 (tppp) cc_final: 0.7846 (tptp)
REVERT: C   36 MET cc_start: 0.4374 (tpt) cc_final: 0.4124 (tpt)
REVERT: C   95 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7429 (mm-30)
REVERT: C  158 ARG cc_start: 0.7631 (tpp-160) cc_final: 0.6826 (ptm160)
REVERT: C  169 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7268 (mtpp)
REVERT: C  194 ASP cc_start: 0.8047 (t0) cc_final: 0.7690 (t0)
REVERT: C  278 ASN cc_start: 0.7376 (m-40) cc_final: 0.7124 (m110)
REVERT: C  309 THR cc_start: 0.8245 (m) cc_final: 0.7887 (m)
REVERT: C  368 LYS cc_start: 0.8377 (tppp) cc_final: 0.7837 (tptp)
REVERT: D   95 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7430 (mm-30)
REVERT: D  169 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7644 (mtmm)
REVERT: D  194 ASP cc_start: 0.8021 (t0) cc_final: 0.7706 (t0)
REVERT: D  278 ASN cc_start: 0.7387 (m-40) cc_final: 0.7142 (m110)
REVERT: D  309 THR cc_start: 0.8226 (m) cc_final: 0.7864 (m)
REVERT: D  368 LYS cc_start: 0.8345 (tppp) cc_final: 0.7817 (tptp)
  outliers start: 42
  outliers final: 34
  residues processed: 181
  average time/residue: 0.5730
  time to fit residues: 115.5067
Evaluate side-chains
  194 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  119 CYS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  207 ASN
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  497 MET
Chi-restraints excluded: chain B residue  508 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  119 CYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  119 CYS
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain D residue  497 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 153 optimal weight:    2.9990
   chunk 166 optimal weight:    0.0980
   chunk 178 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 155 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 181 ASN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 157 ASN
C 181 ASN
** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.155866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.104559 restraints weight = 16953.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.23
r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15572  Z= 0.133
  Angle     :  0.503  10.423  21044  Z= 0.268
  Chirality :  0.038   0.138   2364
  Planarity :  0.004   0.066   2572
  Dihedral  :  9.267  80.690   2096
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.29 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.07 (0.20), residues: 1804
  helix:  3.24 (0.14), residues: 1096
  sheet:  1.69 (0.34), residues: 220
  loop : -0.80 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B  59 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.013   0.001   PHE C 494 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (15564)
  covalent geometry    : angle       0.50313 (21028)
  SS BOND              : bond        0.00105 (    8)
  SS BOND              : angle       0.30325 (   16)
  hydrogen bonds       : bond        0.04415 ( 1061)
  hydrogen bonds       : angle       4.01577 ( 3375)

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

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

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3608 Ramachandran restraints generated.
    1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 172
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: A  158 ARG cc_start: 0.7528 (tpp-160) cc_final: 0.6730 (ptm160)
REVERT: A  169 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7305 (mtpp)
REVERT: A  309 THR cc_start: 0.8224 (m) cc_final: 0.7866 (m)
REVERT: A  349 LEU cc_start: 0.8004 (tp) cc_final: 0.7709 (tt)
REVERT: A  368 LYS cc_start: 0.8338 (tppp) cc_final: 0.7823 (tptp)
REVERT: A  508 ASP cc_start: 0.8191 (t0) cc_final: 0.7916 (m-30)
REVERT: B   50 MET cc_start: 0.7574 (ptm) cc_final: 0.6951 (ptm)
REVERT: B   54 GLU cc_start: 0.7848 (tt0) cc_final: 0.7447 (tm-30)
REVERT: B   95 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7435 (mm-30)
REVERT: B  158 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.6744 (ptm160)
REVERT: B  169 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7283 (mtpp)
REVERT: B  194 ASP cc_start: 0.8017 (t0) cc_final: 0.7652 (t0)
REVERT: B  278 ASN cc_start: 0.7412 (m-40) cc_final: 0.7150 (m110)
REVERT: B  309 THR cc_start: 0.8218 (m) cc_final: 0.7862 (m)
REVERT: B  349 LEU cc_start: 0.8017 (tp) cc_final: 0.7717 (tt)
REVERT: B  368 LYS cc_start: 0.8403 (tppp) cc_final: 0.7877 (tptp)
REVERT: C   95 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7411 (mm-30)
REVERT: C  158 ARG cc_start: 0.7636 (tpp-160) cc_final: 0.6837 (ptm160)
REVERT: C  169 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7312 (mtpp)
REVERT: C  194 ASP cc_start: 0.8037 (t0) cc_final: 0.7683 (t0)
REVERT: C  278 ASN cc_start: 0.7378 (m-40) cc_final: 0.7124 (m110)
REVERT: C  309 THR cc_start: 0.8235 (m) cc_final: 0.7880 (m)
REVERT: C  368 LYS cc_start: 0.8393 (tppp) cc_final: 0.7864 (tptp)
REVERT: D   95 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7433 (mm-30)
REVERT: D  158 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.6784 (ptm160)
REVERT: D  169 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7656 (mtmm)
REVERT: D  194 ASP cc_start: 0.8066 (t0) cc_final: 0.7703 (t0)
REVERT: D  278 ASN cc_start: 0.7388 (m-40) cc_final: 0.7131 (m110)
REVERT: D  309 THR cc_start: 0.8221 (m) cc_final: 0.7858 (m)
REVERT: D  368 LYS cc_start: 0.8346 (tppp) cc_final: 0.7822 (tptp)
  outliers start: 41
  outliers final: 30
  residues processed: 191
  average time/residue: 0.5508
  time to fit residues: 117.6261
Evaluate side-chains
  193 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  119 CYS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  119 CYS
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  209 SER
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  367 ILE
Chi-restraints excluded: chain C residue  497 MET
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  119 CYS
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  209 SER
Chi-restraints excluded: chain D residue  290 VAL
Chi-restraints excluded: chain D residue  497 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 145 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 138 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 150 optimal weight:    0.8980
   chunk 171 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 181 ASN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 ASN
B 181 ASN
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 157 ASN
C 181 ASN
** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.156141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.105457 restraints weight = 16755.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.20
r_work: 0.3072 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15572  Z= 0.125
  Angle     :  0.494  10.127  21044  Z= 0.264
  Chirality :  0.038   0.134   2364
  Planarity :  0.004   0.067   2572
  Dihedral  :  9.039  77.298   2096
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.65 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.20), residues: 1804
  helix:  3.28 (0.14), residues: 1096
  sheet:  1.70 (0.34), residues: 220
  loop : -0.96 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C  59 
 TYR   0.014   0.001   TYR B 486 
 PHE   0.015   0.001   PHE D 502 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (15564)
  covalent geometry    : angle       0.49424 (21028)
  SS BOND              : bond        0.00097 (    8)
  SS BOND              : angle       0.28852 (   16)
  hydrogen bonds       : bond        0.04270 ( 1061)
  hydrogen bonds       : angle       3.98319 ( 3375)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5788.22 seconds
wall clock time: 99 minutes 22.75 seconds (5962.75 seconds total)