Starting phenix.real_space_refine
on Thu Sep 18 08:30:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ekz_48142/09_2025/9ekz_48142.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ekz_48142/09_2025/9ekz_48142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ekz_48142/09_2025/9ekz_48142.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ekz_48142/09_2025/9ekz_48142.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ekz_48142/09_2025/9ekz_48142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ekz_48142/09_2025/9ekz_48142.map"
  }
  resolution = 2.61
  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=   0.032
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   10080      2.51       5
     N    2428      2.21       5
     O    2708      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: 15312
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3798
          Classifications: {'peptide': 461}
          Link IDs: {'PTRANS': 7, 'TRANS': 453}
          Chain breaks: 3
    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: 3.62, per 1000 atoms: 0.24
  Number of scatterers: 15312
  At special positions: 0
  Unit cell: (115.128, 115.128, 118.872, 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    2708      8.00
     N    2428      7.00
     C   10080      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=2.02
    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=2.02
    Simple disulfide: pdb=" SG  CYS C 243 " - pdb=" SG  CYS C 274 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 243 " - pdb=" SG  CYS D 274 " distance=2.02

  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: 0.96
  Conformation dependent library (CDL) restraints added in 658.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3528

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 8 sheets defined
      68.6% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 49
    Processing helix  chain 'A' and resid 51 through 60
    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: 3.572A  pdb=" N   ARG A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 238
      removed outlier: 3.514A  pdb=" N   ILE A 235 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   HIS A 236 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 329
      removed outlier: 3.759A  pdb=" N   GLU A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 371
      removed outlier: 3.720A  pdb=" N   VAL A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 393
    Processing helix  chain 'A' and resid 393 through 400
      removed outlier: 3.612A  pdb=" N   LEU A 397 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE A 400 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 440
      removed outlier: 5.044A  pdb=" N   LEU A 406 " --> pdb=" O   ALA A 402 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE A 407 " --> pdb=" O   TYR A 403 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      Proline residue:  A 415  - end of helix
      removed outlier: 3.729A  pdb=" N   CYS A 423 " --> pdb=" O   ARG A 419 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   MET A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 427 " --> pdb=" O   CYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 443
      No H-bonds generated for 'chain 'A' and resid 441 through 443'
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 464 through 471
    Processing helix  chain 'A' and resid 476 through 497
    Processing helix  chain 'A' and resid 497 through 519
    Processing helix  chain 'B' and resid 37 through 49
    Processing helix  chain 'B' and resid 51 through 60
    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: 3.571A  pdb=" N   ARG B 212 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 238
      removed outlier: 3.514A  pdb=" N   ILE B 235 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   HIS B 236 " --> pdb=" O   GLN B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 329
      removed outlier: 3.759A  pdb=" N   GLU B 328 " --> pdb=" O   ASN B 324 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS B 329 " --> pdb=" O   PHE B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 371
      removed outlier: 3.720A  pdb=" N   VAL B 348 " --> pdb=" O   ASN B 344 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 349 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 393
    Processing helix  chain 'B' and resid 393 through 400
      removed outlier: 3.611A  pdb=" N   LEU B 397 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE B 400 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 440
      removed outlier: 5.044A  pdb=" N   LEU B 406 " --> pdb=" O   ALA B 402 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE B 407 " --> pdb=" O   TYR B 403 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET B 410 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      Proline residue:  B 415  - end of helix
      removed outlier: 3.729A  pdb=" N   CYS B 423 " --> pdb=" O   ARG B 419 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET B 426 " --> pdb=" O   ALA B 422 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE B 427 " --> pdb=" O   CYS B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 443
      No H-bonds generated for 'chain 'B' and resid 441 through 443'
    Processing helix  chain 'B' and resid 448 through 461
    Processing helix  chain 'B' and resid 464 through 471
    Processing helix  chain 'B' and resid 476 through 497
    Processing helix  chain 'B' and resid 497 through 519
    Processing helix  chain 'C' and resid 37 through 49
    Processing helix  chain 'C' and resid 51 through 60
    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: 3.571A  pdb=" N   ARG C 212 " --> pdb=" O   SER C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 238
      removed outlier: 3.514A  pdb=" N   ILE C 235 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   HIS C 236 " --> pdb=" O   GLN C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 329
      removed outlier: 3.759A  pdb=" N   GLU C 328 " --> pdb=" O   ASN C 324 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS C 329 " --> pdb=" O   PHE C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 371
      removed outlier: 3.720A  pdb=" N   VAL C 348 " --> pdb=" O   ASN C 344 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU C 349 " --> pdb=" O   GLY C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 393
    Processing helix  chain 'C' and resid 393 through 400
      removed outlier: 3.611A  pdb=" N   LEU C 397 " --> pdb=" O   VAL C 393 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   PHE C 400 " --> pdb=" O   TYR C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 400 through 440
      removed outlier: 5.044A  pdb=" N   LEU C 406 " --> pdb=" O   ALA C 402 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE C 407 " --> pdb=" O   TYR C 403 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET C 410 " --> pdb=" O   LEU C 406 " (cutoff:3.500A)
      Proline residue:  C 415  - end of helix
      removed outlier: 3.728A  pdb=" N   CYS C 423 " --> pdb=" O   ARG C 419 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   MET C 426 " --> pdb=" O   ALA C 422 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE C 427 " --> pdb=" O   CYS C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 441 through 443
      No H-bonds generated for 'chain 'C' and resid 441 through 443'
    Processing helix  chain 'C' and resid 448 through 461
    Processing helix  chain 'C' and resid 464 through 471
    Processing helix  chain 'C' and resid 476 through 497
    Processing helix  chain 'C' and resid 497 through 519
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 51 through 60
    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: 3.572A  pdb=" N   ARG D 212 " --> pdb=" O   SER D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 238
      removed outlier: 3.515A  pdb=" N   ILE D 235 " --> pdb=" O   LEU D 232 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   HIS D 236 " --> pdb=" O   GLN D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 329
      removed outlier: 3.759A  pdb=" N   GLU D 328 " --> pdb=" O   ASN D 324 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS D 329 " --> pdb=" O   PHE D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 344 through 371
      removed outlier: 3.720A  pdb=" N   VAL D 348 " --> pdb=" O   ASN D 344 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU D 349 " --> pdb=" O   GLY D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 375 through 393
    Processing helix  chain 'D' and resid 393 through 400
      removed outlier: 3.611A  pdb=" N   LEU D 397 " --> pdb=" O   VAL D 393 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE D 400 " --> pdb=" O   TYR D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 400 through 440
      removed outlier: 5.043A  pdb=" N   LEU D 406 " --> pdb=" O   ALA D 402 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE D 407 " --> pdb=" O   TYR D 403 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET D 410 " --> pdb=" O   LEU D 406 " (cutoff:3.500A)
      Proline residue:  D 415  - end of helix
      removed outlier: 3.728A  pdb=" N   CYS D 423 " --> pdb=" O   ARG D 419 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   MET D 426 " --> pdb=" O   ALA D 422 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE D 427 " --> pdb=" O   CYS D 423 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 441 through 443
      No H-bonds generated for 'chain 'D' and resid 441 through 443'
    Processing helix  chain 'D' and resid 448 through 461
    Processing helix  chain 'D' and resid 464 through 471
    Processing helix  chain 'D' and resid 476 through 497
    Processing helix  chain 'D' and resid 497 through 519
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121
      removed outlier: 4.153A  pdb=" N   CYS A 243 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121
      removed outlier: 4.153A  pdb=" N   CYS A 243 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A 218 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN A 220 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   HIS A 226 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 6.820A  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: 4.154A  pdb=" N   CYS B 243 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121
      removed outlier: 4.154A  pdb=" N   CYS B 243 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU B 218 " --> pdb=" O   TYR B 168 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TYR B 168 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN B 220 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   HIS B 226 " --> pdb=" O   GLY B 160 " (cutoff:3.500A)
      removed outlier: 6.820A  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: 4.153A  pdb=" N   CYS C 243 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121
      removed outlier: 4.153A  pdb=" N   CYS C 243 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU C 218 " --> pdb=" O   TYR C 168 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   TYR C 168 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN C 220 " --> pdb=" O   GLN C 166 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   HIS C 226 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 6.819A  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: 4.154A  pdb=" N   CYS D 243 " --> pdb=" O   GLU D 272 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121
      removed outlier: 4.154A  pdb=" N   CYS D 243 " --> pdb=" O   GLU D 272 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU D 218 " --> pdb=" O   TYR D 168 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TYR D 168 " --> pdb=" O   LEU D 218 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN D 220 " --> pdb=" O   GLN D 166 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   HIS D 226 " --> pdb=" O   GLY D 160 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   GLY D 160 " --> pdb=" O   HIS D 226 " (cutoff:3.500A)

    1181 hydrogen bonds defined for protein.
    3447 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: 2.71

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4645
        1.35 -     1.47: 3897
        1.47 -     1.60: 6986
        1.60 -     1.73: 0
        1.73 -     1.85: 136
  Bond restraints: 15664
  Sorted by residual:
  bond pdb=" C   ILE B 503 "
       pdb=" N   ALA B 504 "
    ideal  model  delta    sigma   weight residual
    1.335  1.241  0.094 1.31e-02 5.83e+03 5.13e+01
  bond pdb=" C   ILE A 503 "
       pdb=" N   ALA A 504 "
    ideal  model  delta    sigma   weight residual
    1.335  1.241  0.094 1.31e-02 5.83e+03 5.10e+01
  bond pdb=" C   ILE C 503 "
       pdb=" N   ALA C 504 "
    ideal  model  delta    sigma   weight residual
    1.335  1.242  0.093 1.31e-02 5.83e+03 5.06e+01
  bond pdb=" C   ILE D 503 "
       pdb=" N   ALA D 504 "
    ideal  model  delta    sigma   weight residual
    1.335  1.242  0.093 1.31e-02 5.83e+03 4.99e+01
  bond pdb=" C16 ZB4 A 601 "
       pdb=" N02 ZB4 A 601 "
    ideal  model  delta    sigma   weight residual
    1.468  1.353  0.115 2.00e-02 2.50e+03 3.33e+01
  ... (remaining 15659 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.78: 20980
        3.78 -     7.56: 152
        7.56 -    11.34: 24
       11.34 -    15.12: 4
       15.12 -    18.90: 4
  Bond angle restraints: 21164
  Sorted by residual:
  angle pdb=" O   ILE B 503 "
        pdb=" C   ILE B 503 "
        pdb=" N   ALA B 504 "
      ideal   model   delta    sigma   weight residual
     121.87  130.98   -9.11 9.70e-01 1.06e+00 8.83e+01
  angle pdb=" O   ILE D 503 "
        pdb=" C   ILE D 503 "
        pdb=" N   ALA D 504 "
      ideal   model   delta    sigma   weight residual
     121.87  130.98   -9.11 9.70e-01 1.06e+00 8.82e+01
  angle pdb=" O   ILE A 503 "
        pdb=" C   ILE A 503 "
        pdb=" N   ALA A 504 "
      ideal   model   delta    sigma   weight residual
     121.87  130.97   -9.10 9.70e-01 1.06e+00 8.81e+01
  angle pdb=" O   ILE C 503 "
        pdb=" C   ILE C 503 "
        pdb=" N   ALA C 504 "
      ideal   model   delta    sigma   weight residual
     121.87  130.95   -9.08 9.70e-01 1.06e+00 8.77e+01
  angle pdb=" CA  ILE D 503 "
        pdb=" C   ILE D 503 "
        pdb=" N   ALA D 504 "
      ideal   model   delta    sigma   weight residual
     117.15  108.10    9.05 1.14e+00 7.69e-01 6.31e+01
  ... (remaining 21159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.53: 9036
       35.53 -    71.05: 224
       71.05 -   106.58: 16
      106.58 -   142.11: 4
      142.11 -   177.63: 8
  Dihedral angle restraints: 9288
    sinusoidal: 3828
      harmonic: 5460
  Sorted by residual:
  dihedral pdb=" C   TYR D 510 "
           pdb=" N   TYR D 510 "
           pdb=" CA  TYR D 510 "
           pdb=" CB  TYR D 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.14  -13.46     0      2.50e+00 1.60e-01 2.90e+01
  dihedral pdb=" C   TYR A 510 "
           pdb=" N   TYR A 510 "
           pdb=" CA  TYR A 510 "
           pdb=" CB  TYR A 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.17  -13.43     0      2.50e+00 1.60e-01 2.89e+01
  dihedral pdb=" C   TYR C 510 "
           pdb=" N   TYR C 510 "
           pdb=" CA  TYR C 510 "
           pdb=" CB  TYR C 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.19  -13.41     0      2.50e+00 1.60e-01 2.88e+01
  ... (remaining 9285 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1924
       0.060 -    0.120: 352
       0.120 -    0.180: 72
       0.180 -    0.240: 8
       0.240 -    0.300: 16
  Chirality restraints: 2372
  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    2.81   -0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CA  LEU B 372 "
            pdb=" N   LEU B 372 "
            pdb=" C   LEU B 372 "
            pdb=" CB  LEU B 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.22e+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    2.81   -0.30 2.00e-01 2.50e+01 2.20e+00
  ... (remaining 2369 not shown)

  Planarity restraints: 2592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR D 510 "   -0.020 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   TYR D 510 "    0.068 2.00e-02 2.50e+03
        pdb=" O   TYR D 510 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ASP D 511 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 510 "   -0.020 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   TYR C 510 "    0.068 2.00e-02 2.50e+03
        pdb=" O   TYR C 510 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ASP C 511 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 510 "   -0.020 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   TYR A 510 "    0.068 2.00e-02 2.50e+03
        pdb=" O   TYR A 510 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ASP A 511 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 2589 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 4640
        2.83 -     3.35: 14503
        3.35 -     3.86: 25408
        3.86 -     4.38: 30070
        4.38 -     4.90: 51064
  Nonbonded interactions: 125685
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 376 "
            pdb=" OH  TYR D 442 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   PHE C 469 "
            pdb=" NH2 ARG C 484 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   PHE B 469 "
            pdb=" NH2 ARG B 484 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   PHE A 469 "
            pdb=" NH2 ARG A 484 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   PHE D 469 "
            pdb=" NH2 ARG D 484 "
     model   vdw
     2.332 3.120
  ... (remaining 125680 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: 0.04
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:             3.340
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.120
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:9.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
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   0.115  15672  Z= 0.461
  Angle     :  0.943  18.897  21180  Z= 0.605
  Chirality :  0.055   0.300   2372
  Planarity :  0.007   0.128   2592
  Dihedral  : 16.502 177.634   5736
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.40 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.51 %
  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:  1.33 (0.19), residues: 1812
  helix:  1.48 (0.15), residues: 1148
  sheet:  1.29 (0.33), residues: 220
  loop : -0.84 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 310 
 TYR   0.021   0.002   TYR B 375 
 PHE   0.019   0.002   PHE B 502 
 TRP   0.011   0.002   TRP C  64 
 HIS   0.005   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00812 (15664)
  covalent geometry    : angle       0.94299 (21164)
  SS BOND              : bond        0.00910 (    8)
  SS BOND              : angle       1.35181 (   16)
  hydrogen bonds       : bond        0.17383 ( 1081)
  hydrogen bonds       : angle       6.89560 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 248
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 TYR cc_start: 0.7740 (t80) cc_final: 0.7360 (t80)
REVERT: A  159 ILE cc_start: 0.8676 (mt) cc_final: 0.7984 (mm)
REVERT: A  266 ASP cc_start: 0.7910 (m-30) cc_final: 0.7470 (t70)
REVERT: A  272 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7633 (pp20)
REVERT: A  309 THR cc_start: 0.7776 (m) cc_final: 0.7492 (p)
REVERT: A  447 GLU cc_start: 0.8207 (pt0) cc_final: 0.7991 (mt-10)
REVERT: A  471 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7887 (mt0)
REVERT: B   47 PHE cc_start: 0.7284 (t80) cc_final: 0.6957 (t80)
REVERT: B   48 TYR cc_start: 0.7491 (t80) cc_final: 0.7170 (t80)
REVERT: B  157 ASN cc_start: 0.7178 (t0) cc_final: 0.6965 (m-40)
REVERT: B  159 ILE cc_start: 0.8710 (mt) cc_final: 0.8065 (mm)
REVERT: B  266 ASP cc_start: 0.7907 (m-30) cc_final: 0.7466 (t70)
REVERT: B  272 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7622 (pp20)
REVERT: B  309 THR cc_start: 0.8090 (m) cc_final: 0.7771 (p)
REVERT: B  410 MET cc_start: 0.7740 (mtm) cc_final: 0.7530 (mtm)
REVERT: B  447 GLU cc_start: 0.8196 (pt0) cc_final: 0.7875 (mt-10)
REVERT: B  471 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7835 (mt0)
REVERT: B  509 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.7016 (p)
REVERT: C   47 PHE cc_start: 0.7285 (t80) cc_final: 0.7024 (t80)
REVERT: C   48 TYR cc_start: 0.7701 (t80) cc_final: 0.7393 (t80)
REVERT: C  159 ILE cc_start: 0.8716 (mt) cc_final: 0.8044 (mm)
REVERT: C  266 ASP cc_start: 0.7876 (m-30) cc_final: 0.7403 (t70)
REVERT: C  272 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7600 (pp20)
REVERT: C  300 ILE cc_start: 0.7315 (mm) cc_final: 0.7070 (mt)
REVERT: C  309 THR cc_start: 0.8039 (m) cc_final: 0.7696 (p)
REVERT: C  410 MET cc_start: 0.7744 (mtm) cc_final: 0.7516 (mtm)
REVERT: C  447 GLU cc_start: 0.8163 (pt0) cc_final: 0.7959 (mt-10)
REVERT: C  471 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7856 (tt0)
REVERT: C  509 SER cc_start: 0.7187 (OUTLIER) cc_final: 0.6951 (p)
REVERT: D   47 PHE cc_start: 0.7430 (t80) cc_final: 0.7224 (t80)
REVERT: D   48 TYR cc_start: 0.7742 (t80) cc_final: 0.7438 (t80)
REVERT: D  159 ILE cc_start: 0.8681 (mt) cc_final: 0.8263 (mm)
REVERT: D  266 ASP cc_start: 0.7889 (m-30) cc_final: 0.7414 (t70)
REVERT: D  272 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7601 (pp20)
REVERT: D  309 THR cc_start: 0.8017 (m) cc_final: 0.7686 (p)
REVERT: D  447 GLU cc_start: 0.8213 (pt0) cc_final: 0.7975 (mt-10)
REVERT: D  471 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7817 (mt0)
  outliers start: 16
  outliers final: 10
  residues processed: 264
  average time/residue: 0.5572
  time to fit residues: 164.4631
Evaluate side-chains
  213 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  509 SER
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain B residue  509 SER
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain C residue  509 SER
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain C residue  519 ASN
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  519 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 167 HIS
A 184 ASN
A 517 GLN
B  69 GLN
B 167 HIS
B 184 ASN
B 517 GLN
C  69 GLN
C 167 HIS
C 184 ASN
C 517 GLN
D  69 GLN
D 167 HIS
D 184 ASN
D 517 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.153504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.103500 restraints weight = 16960.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.16
r_work: 0.3046 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
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: 0.7801
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15672  Z= 0.141
  Angle     :  0.523   7.177  21180  Z= 0.281
  Chirality :  0.040   0.198   2372
  Planarity :  0.004   0.048   2592
  Dihedral  : 13.415 154.099   2128
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.78 %
    Favored  : 84.56 %
  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:  2.27 (0.19), residues: 1812
  helix:  2.29 (0.15), residues: 1168
  sheet:  1.58 (0.31), residues: 200
  loop : -0.72 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 212 
 TYR   0.013   0.001   TYR A 264 
 PHE   0.022   0.002   PHE A 502 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (15664)
  covalent geometry    : angle       0.52284 (21164)
  SS BOND              : bond        0.00146 (    8)
  SS BOND              : angle       0.29126 (   16)
  hydrogen bonds       : bond        0.04910 ( 1081)
  hydrogen bonds       : angle       4.47228 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 213
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6967 (mp)
REVERT: A   48 TYR cc_start: 0.7612 (t80) cc_final: 0.7360 (t80)
REVERT: A  159 ILE cc_start: 0.8558 (mt) cc_final: 0.7970 (mm)
REVERT: A  169 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7511 (ptmt)
REVERT: A  266 ASP cc_start: 0.7748 (m-30) cc_final: 0.7165 (t70)
REVERT: A  372 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6553 (mt)
REVERT: A  447 GLU cc_start: 0.8187 (pt0) cc_final: 0.7977 (mt-10)
REVERT: A  471 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7868 (mt0)
REVERT: A  475 LYS cc_start: 0.8172 (pttm) cc_final: 0.7669 (mttt)
REVERT: B   45 LEU cc_start: 0.7200 (tp) cc_final: 0.6911 (mp)
REVERT: B   48 TYR cc_start: 0.7530 (t80) cc_final: 0.7236 (t80)
REVERT: B  159 ILE cc_start: 0.8578 (mt) cc_final: 0.8033 (mm)
REVERT: B  266 ASP cc_start: 0.7725 (m-30) cc_final: 0.7144 (t70)
REVERT: B  447 GLU cc_start: 0.8133 (pt0) cc_final: 0.7892 (mt-10)
REVERT: B  471 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7870 (mt0)
REVERT: C   45 LEU cc_start: 0.7106 (tp) cc_final: 0.6845 (mp)
REVERT: C   48 TYR cc_start: 0.7582 (t80) cc_final: 0.7282 (t80)
REVERT: C   60 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7398 (tpp-160)
REVERT: C   75 MET cc_start: 0.7751 (mtm) cc_final: 0.7518 (mmm)
REVERT: C  159 ILE cc_start: 0.8574 (mt) cc_final: 0.8280 (mm)
REVERT: C  231 ASP cc_start: 0.7446 (p0) cc_final: 0.6866 (t0)
REVERT: C  266 ASP cc_start: 0.7713 (m-30) cc_final: 0.7140 (t70)
REVERT: C  300 ILE cc_start: 0.7243 (mm) cc_final: 0.7012 (mt)
REVERT: C  447 GLU cc_start: 0.8154 (pt0) cc_final: 0.7951 (mt-10)
REVERT: C  471 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7824 (mt0)
REVERT: D   45 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6870 (mp)
REVERT: D   48 TYR cc_start: 0.7591 (t80) cc_final: 0.7300 (t80)
REVERT: D   60 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7449 (tpp-160)
REVERT: D  159 ILE cc_start: 0.8547 (mt) cc_final: 0.7970 (mm)
REVERT: D  169 LYS cc_start: 0.7906 (ptmt) cc_final: 0.7532 (ptmt)
REVERT: D  231 ASP cc_start: 0.7437 (p0) cc_final: 0.6842 (t0)
REVERT: D  266 ASP cc_start: 0.7732 (m-30) cc_final: 0.7137 (t70)
REVERT: D  471 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7842 (mt0)
  outliers start: 28
  outliers final: 12
  residues processed: 228
  average time/residue: 0.5430
  time to fit residues: 138.7631
Evaluate side-chains
  200 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 185
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain C residue  519 ASN
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  519 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 144 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 137 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 181 optimal weight:    0.8980
   chunk 147 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 411 GLN
B 411 GLN
C 411 GLN
D 411 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.153463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.102894 restraints weight = 16938.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.20
r_work: 0.3034 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    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 = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15672  Z= 0.136
  Angle     :  0.494   8.625  21180  Z= 0.264
  Chirality :  0.040   0.197   2372
  Planarity :  0.003   0.048   2592
  Dihedral  : 12.874 145.105   2124
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.73 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.67 (0.20), residues: 1812
  helix:  2.64 (0.15), residues: 1168
  sheet:  1.67 (0.31), residues: 200
  loop : -0.65 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 212 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.018   0.001   PHE A 502 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (15664)
  covalent geometry    : angle       0.49447 (21164)
  SS BOND              : bond        0.00084 (    8)
  SS BOND              : angle       0.27196 (   16)
  hydrogen bonds       : bond        0.04689 ( 1081)
  hydrogen bonds       : angle       4.21037 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 191
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6928 (mp)
REVERT: A  159 ILE cc_start: 0.8515 (mt) cc_final: 0.8196 (mm)
REVERT: A  231 ASP cc_start: 0.7426 (p0) cc_final: 0.7006 (t0)
REVERT: A  266 ASP cc_start: 0.7729 (m-30) cc_final: 0.7083 (t70)
REVERT: A  273 GLU cc_start: 0.7375 (pm20) cc_final: 0.7170 (pm20)
REVERT: A  372 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6655 (mt)
REVERT: A  410 MET cc_start: 0.7742 (mtm) cc_final: 0.7340 (mtp)
REVERT: A  471 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: B   45 LEU cc_start: 0.7180 (tp) cc_final: 0.6892 (mp)
REVERT: B   48 TYR cc_start: 0.7521 (t80) cc_final: 0.7287 (t80)
REVERT: B   54 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7363 (mt-10)
REVERT: B  159 ILE cc_start: 0.8571 (mt) cc_final: 0.8240 (mm)
REVERT: B  266 ASP cc_start: 0.7710 (m-30) cc_final: 0.7063 (t70)
REVERT: B  300 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7074 (mt)
REVERT: B  410 MET cc_start: 0.7756 (mtm) cc_final: 0.7366 (mtp)
REVERT: B  471 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: C   45 LEU cc_start: 0.7238 (tp) cc_final: 0.6899 (mp)
REVERT: C   48 TYR cc_start: 0.7527 (t80) cc_final: 0.7276 (t80)
REVERT: C   60 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7484 (tpp-160)
REVERT: C   75 MET cc_start: 0.7637 (mtm) cc_final: 0.7260 (mmm)
REVERT: C  159 ILE cc_start: 0.8559 (mt) cc_final: 0.8235 (mm)
REVERT: C  231 ASP cc_start: 0.7398 (p0) cc_final: 0.7024 (t0)
REVERT: C  266 ASP cc_start: 0.7728 (m-30) cc_final: 0.7086 (t70)
REVERT: C  410 MET cc_start: 0.7701 (mtm) cc_final: 0.7307 (mtp)
REVERT: C  471 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: D   45 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6773 (mp)
REVERT: D   60 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7403 (tpp-160)
REVERT: D  159 ILE cc_start: 0.8539 (mt) cc_final: 0.8205 (mm)
REVERT: D  231 ASP cc_start: 0.7341 (p0) cc_final: 0.7095 (t0)
REVERT: D  266 ASP cc_start: 0.7732 (m-30) cc_final: 0.7079 (t70)
REVERT: D  300 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7081 (mt)
REVERT: D  471 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7783 (tt0)
  outliers start: 49
  outliers final: 17
  residues processed: 225
  average time/residue: 0.5163
  time to fit residues: 131.1538
Evaluate side-chains
  197 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  368 LYS
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain C residue  368 LYS
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain C residue  519 ASN
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  519 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0270
   chunk 172 optimal weight:    8.9990
   chunk 174 optimal weight:    5.9990
   chunk 183 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 179 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    2.2046

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
A 411 GLN
B 167 HIS
C 167 HIS
D 167 HIS
D 411 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.098585 restraints weight = 17001.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.21
r_work: 0.2975 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032  15672  Z= 0.234
  Angle     :  0.579   7.880  21180  Z= 0.307
  Chirality :  0.043   0.180   2372
  Planarity :  0.004   0.046   2592
  Dihedral  : 12.352 135.927   2124
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.26 %
    Favored  : 81.00 %
  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:  2.45 (0.19), residues: 1812
  helix:  2.47 (0.15), residues: 1160
  sheet:  1.64 (0.31), residues: 200
  loop : -0.74 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  60 
 TYR   0.027   0.002   TYR A  48 
 PHE   0.015   0.002   PHE D 502 
 TRP   0.009   0.001   TRP B  64 
 HIS   0.004   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (15664)
  covalent geometry    : angle       0.57883 (21164)
  SS BOND              : bond        0.00149 (    8)
  SS BOND              : angle       0.47137 (   16)
  hydrogen bonds       : bond        0.05696 ( 1081)
  hydrogen bonds       : angle       4.45115 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 176
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7220 (mp)
REVERT: A  159 ILE cc_start: 0.8660 (mt) cc_final: 0.8322 (mm)
REVERT: A  266 ASP cc_start: 0.7891 (m-30) cc_final: 0.7312 (t70)
REVERT: A  273 GLU cc_start: 0.7599 (pm20) cc_final: 0.7377 (pm20)
REVERT: A  372 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6792 (mt)
REVERT: A  410 MET cc_start: 0.7907 (mtm) cc_final: 0.7457 (mtp)
REVERT: A  471 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7929 (mt0)
REVERT: B   54 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7352 (mt-10)
REVERT: B   87 ASN cc_start: 0.7783 (p0) cc_final: 0.7528 (p0)
REVERT: B  159 ILE cc_start: 0.8697 (mt) cc_final: 0.8360 (mm)
REVERT: B  266 ASP cc_start: 0.7868 (m-30) cc_final: 0.7280 (t70)
REVERT: B  410 MET cc_start: 0.7909 (mtm) cc_final: 0.7463 (mtp)
REVERT: B  471 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7903 (mt0)
REVERT: C   45 LEU cc_start: 0.7378 (tp) cc_final: 0.7150 (mm)
REVERT: C   60 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7435 (tpp-160)
REVERT: C  159 ILE cc_start: 0.8700 (mt) cc_final: 0.8358 (mm)
REVERT: C  266 ASP cc_start: 0.7910 (m-30) cc_final: 0.7334 (t70)
REVERT: C  410 MET cc_start: 0.7829 (mtm) cc_final: 0.7394 (mtp)
REVERT: C  471 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7909 (mt0)
REVERT: D   45 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7119 (mp)
REVERT: D   60 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7428 (tpp-160)
REVERT: D   87 ASN cc_start: 0.7813 (p0) cc_final: 0.7526 (p0)
REVERT: D  159 ILE cc_start: 0.8677 (mt) cc_final: 0.8334 (mm)
REVERT: D  266 ASP cc_start: 0.7882 (m-30) cc_final: 0.7290 (t70)
REVERT: D  410 MET cc_start: 0.7928 (mtm) cc_final: 0.7477 (mtp)
REVERT: D  471 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7971 (mt0)
  outliers start: 63
  outliers final: 35
  residues processed: 218
  average time/residue: 0.5121
  time to fit residues: 125.9180
Evaluate side-chains
  209 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 171
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  368 LYS
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  513 ILE
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain C residue  181 ASN
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  368 LYS
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain C residue  513 ILE
Chi-restraints excluded: chain C residue  519 ASN
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  313 VAL
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  519 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 125 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 124 optimal weight:    0.8980
   chunk 165 optimal weight:    0.0270
   chunk 79 optimal weight:    0.6980
   chunk 92 optimal weight:   20.0000
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
A 411 GLN
B 167 HIS
B 411 GLN
C 167 HIS
C 411 GLN
D 167 HIS
D 411 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.155324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.104593 restraints weight = 17059.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.22
r_work: 0.3054 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
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: 0.7882
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  15672  Z= 0.117
  Angle     :  0.484   7.504  21180  Z= 0.254
  Chirality :  0.039   0.137   2372
  Planarity :  0.003   0.047   2592
  Dihedral  : 11.198 115.971   2124
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.91 %
    Favored  : 80.88 %
  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:  2.91 (0.20), residues: 1812
  helix:  2.88 (0.15), residues: 1148
  sheet:  1.52 (0.31), residues: 200
  loop : -0.44 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  60 
 TYR   0.025   0.001   TYR C  48 
 PHE   0.015   0.001   PHE B 502 
 TRP   0.009   0.001   TRP C  64 
 HIS   0.002   0.000   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (15664)
  covalent geometry    : angle       0.48393 (21164)
  SS BOND              : bond        0.00070 (    8)
  SS BOND              : angle       0.26392 (   16)
  hydrogen bonds       : bond        0.04208 ( 1081)
  hydrogen bonds       : angle       4.08353 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 183
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7059 (mp)
REVERT: A   49 PHE cc_start: 0.8296 (m-10) cc_final: 0.8094 (m-10)
REVERT: A  159 ILE cc_start: 0.8643 (mt) cc_final: 0.8315 (mm)
REVERT: A  184 ASN cc_start: 0.7464 (t0) cc_final: 0.7073 (m-40)
REVERT: A  231 ASP cc_start: 0.7422 (p0) cc_final: 0.7160 (t0)
REVERT: A  266 ASP cc_start: 0.7788 (m-30) cc_final: 0.7162 (t70)
REVERT: A  273 GLU cc_start: 0.7568 (pm20) cc_final: 0.7358 (pm20)
REVERT: A  372 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6749 (mt)
REVERT: A  410 MET cc_start: 0.7799 (mtm) cc_final: 0.7390 (mtp)
REVERT: A  471 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: B   46 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7583 (mtmt)
REVERT: B   54 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7340 (mt-10)
REVERT: B   87 ASN cc_start: 0.7277 (p0) cc_final: 0.7051 (p0)
REVERT: B  159 ILE cc_start: 0.8643 (mt) cc_final: 0.8326 (mm)
REVERT: B  231 ASP cc_start: 0.7540 (p0) cc_final: 0.6881 (t0)
REVERT: B  266 ASP cc_start: 0.7776 (m-30) cc_final: 0.7190 (t70)
REVERT: B  410 MET cc_start: 0.7758 (mtm) cc_final: 0.7356 (mtp)
REVERT: B  471 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: C   59 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.5654 (mtm180)
REVERT: C   60 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7506 (tpp-160)
REVERT: C  159 ILE cc_start: 0.8673 (mt) cc_final: 0.8341 (mm)
REVERT: C  266 ASP cc_start: 0.7788 (m-30) cc_final: 0.7203 (t70)
REVERT: C  300 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7151 (mt)
REVERT: C  410 MET cc_start: 0.7762 (mtm) cc_final: 0.7349 (mtp)
REVERT: C  471 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: D   45 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7044 (mp)
REVERT: D   60 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7434 (tpp-160)
REVERT: D   87 ASN cc_start: 0.7384 (p0) cc_final: 0.7178 (p0)
REVERT: D  159 ILE cc_start: 0.8640 (mt) cc_final: 0.8316 (mm)
REVERT: D  184 ASN cc_start: 0.7384 (t0) cc_final: 0.6999 (m-40)
REVERT: D  266 ASP cc_start: 0.7789 (m-30) cc_final: 0.7170 (t70)
REVERT: D  410 MET cc_start: 0.7812 (mtm) cc_final: 0.7392 (mtp)
REVERT: D  471 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7878 (tm-30)
  outliers start: 54
  outliers final: 30
  residues processed: 225
  average time/residue: 0.4547
  time to fit residues: 116.8304
Evaluate side-chains
  202 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ARG
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain C residue   53 CYS
Chi-restraints excluded: chain C residue   59 ARG
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain C residue  519 ASN
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  519 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 151 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 171 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 167 HIS
C 167 HIS
D 167 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.151657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.100737 restraints weight = 17072.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.22
r_work: 0.2996 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    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 = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15672  Z= 0.176
  Angle     :  0.546   8.247  21180  Z= 0.284
  Chirality :  0.040   0.146   2372
  Planarity :  0.003   0.046   2592
  Dihedral  :  9.994  96.821   2124
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.09 %
    Favored  : 80.70 %
  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:  2.83 (0.20), residues: 1812
  helix:  2.80 (0.15), residues: 1148
  sheet:  1.64 (0.31), residues: 200
  loop : -0.48 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 212 
 TYR   0.015   0.001   TYR C 486 
 PHE   0.013   0.002   PHE C 502 
 TRP   0.008   0.001   TRP C 390 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (15664)
  covalent geometry    : angle       0.54588 (21164)
  SS BOND              : bond        0.00097 (    8)
  SS BOND              : angle       0.33961 (   16)
  hydrogen bonds       : bond        0.05033 ( 1081)
  hydrogen bonds       : angle       4.26041 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 174
  time to evaluate  : 0.587 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7203 (mp)
REVERT: A  159 ILE cc_start: 0.8640 (mt) cc_final: 0.8328 (mm)
REVERT: A  184 ASN cc_start: 0.7418 (t0) cc_final: 0.7037 (t0)
REVERT: A  231 ASP cc_start: 0.7636 (p0) cc_final: 0.7021 (t0)
REVERT: A  266 ASP cc_start: 0.7854 (m-30) cc_final: 0.7269 (t70)
REVERT: A  273 GLU cc_start: 0.7579 (pm20) cc_final: 0.7371 (pm20)
REVERT: A  372 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6795 (mt)
REVERT: A  410 MET cc_start: 0.7896 (mtm) cc_final: 0.7407 (mtp)
REVERT: A  471 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7831 (mt0)
REVERT: B   46 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7650 (mtmt)
REVERT: B  159 ILE cc_start: 0.8659 (mt) cc_final: 0.8343 (mm)
REVERT: B  217 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8108 (mtp180)
REVERT: B  266 ASP cc_start: 0.7851 (m-30) cc_final: 0.7265 (t70)
REVERT: B  410 MET cc_start: 0.7832 (mtm) cc_final: 0.7405 (mtp)
REVERT: B  471 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7821 (mt0)
REVERT: C   46 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7606 (mtmt)
REVERT: C   60 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7436 (tpp80)
REVERT: C  159 ILE cc_start: 0.8665 (mt) cc_final: 0.8349 (mm)
REVERT: C  184 ASN cc_start: 0.7629 (t0) cc_final: 0.7368 (m-40)
REVERT: C  217 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8113 (mtp180)
REVERT: C  266 ASP cc_start: 0.7845 (m-30) cc_final: 0.7261 (t70)
REVERT: C  397 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8211 (mp)
REVERT: C  410 MET cc_start: 0.7843 (mtm) cc_final: 0.7406 (mtp)
REVERT: C  471 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7820 (mt0)
REVERT: D   36 MET cc_start: 0.4867 (mmm) cc_final: 0.4371 (mpt)
REVERT: D   45 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7102 (mp)
REVERT: D   60 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7398 (tpp-160)
REVERT: D  159 ILE cc_start: 0.8660 (mt) cc_final: 0.8343 (mm)
REVERT: D  184 ASN cc_start: 0.7504 (t0) cc_final: 0.7112 (m-40)
REVERT: D  217 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8096 (mtp180)
REVERT: D  266 ASP cc_start: 0.7863 (m-30) cc_final: 0.7280 (t70)
REVERT: D  410 MET cc_start: 0.7884 (mtm) cc_final: 0.7423 (mtp)
REVERT: D  471 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7966 (tt0)
  outliers start: 54
  outliers final: 38
  residues processed: 217
  average time/residue: 0.5158
  time to fit residues: 125.7676
Evaluate side-chains
  212 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 165
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  519 ASN
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  447 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  513 ILE
Chi-restraints excluded: chain B residue  519 ASN
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   53 CYS
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain C residue  519 ASN
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  217 ARG
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  519 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 162 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9980
   chunk 175 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 167 optimal weight:    1.9990
   chunk 168 optimal weight:    0.6980
   chunk 108 optimal weight:    0.6980
   chunk 117 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   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 411 GLN
B 411 GLN
D 167 HIS
D 233 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.153852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.103564 restraints weight = 16976.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.20
r_work: 0.3039 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    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 = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15672  Z= 0.126
  Angle     :  0.489   6.943  21180  Z= 0.258
  Chirality :  0.039   0.136   2372
  Planarity :  0.003   0.047   2592
  Dihedral  :  8.662  91.639   2124
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.27 %
    Favored  : 80.88 %
  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:  2.96 (0.20), residues: 1812
  helix:  2.91 (0.15), residues: 1148
  sheet:  1.67 (0.32), residues: 200
  loop : -0.48 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 212 
 TYR   0.013   0.001   TYR C 486 
 PHE   0.013   0.001   PHE C 502 
 TRP   0.008   0.001   TRP B  64 
 HIS   0.002   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (15664)
  covalent geometry    : angle       0.48937 (21164)
  SS BOND              : bond        0.00071 (    8)
  SS BOND              : angle       0.23306 (   16)
  hydrogen bonds       : bond        0.04296 ( 1081)
  hydrogen bonds       : angle       4.07627 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 167
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7173 (mp)
REVERT: A  159 ILE cc_start: 0.8621 (mt) cc_final: 0.8301 (mm)
REVERT: A  184 ASN cc_start: 0.7483 (t0) cc_final: 0.7116 (m-40)
REVERT: A  231 ASP cc_start: 0.7503 (p0) cc_final: 0.7223 (t0)
REVERT: A  266 ASP cc_start: 0.7761 (m-30) cc_final: 0.7174 (t70)
REVERT: A  273 GLU cc_start: 0.7645 (pm20) cc_final: 0.7439 (pm20)
REVERT: A  372 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6764 (mt)
REVERT: A  410 MET cc_start: 0.7868 (mtm) cc_final: 0.7436 (mtp)
REVERT: A  471 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: B   46 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7696 (mtmt)
REVERT: B  159 ILE cc_start: 0.8631 (mt) cc_final: 0.8326 (mm)
REVERT: B  217 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8079 (mtp180)
REVERT: B  266 ASP cc_start: 0.7759 (m-30) cc_final: 0.7131 (t70)
REVERT: B  410 MET cc_start: 0.7817 (mtm) cc_final: 0.7393 (mtp)
REVERT: B  471 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7771 (mt0)
REVERT: C   60 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7485 (tpp80)
REVERT: C  159 ILE cc_start: 0.8649 (mt) cc_final: 0.8327 (mm)
REVERT: C  217 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8060 (mtp180)
REVERT: C  266 ASP cc_start: 0.7741 (m-30) cc_final: 0.7152 (t70)
REVERT: C  410 MET cc_start: 0.7821 (mtm) cc_final: 0.7403 (mtp)
REVERT: C  471 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: D   45 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6941 (mp)
REVERT: D   60 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7443 (tpp80)
REVERT: D  159 ILE cc_start: 0.8640 (mt) cc_final: 0.8323 (mm)
REVERT: D  184 ASN cc_start: 0.7487 (t0) cc_final: 0.7104 (m-40)
REVERT: D  217 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8094 (mtp180)
REVERT: D  266 ASP cc_start: 0.7772 (m-30) cc_final: 0.7148 (t70)
REVERT: D  410 MET cc_start: 0.7844 (mtm) cc_final: 0.7407 (mtp)
REVERT: D  471 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7949 (tt0)
  outliers start: 48
  outliers final: 33
  residues processed: 209
  average time/residue: 0.4956
  time to fit residues: 117.1523
Evaluate side-chains
  198 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 158
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  447 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain C residue   53 CYS
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  217 ARG
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  395 ARG
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  511 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 176 optimal weight:    0.0040
   chunk 118 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 22 optimal weight:    0.4980
   chunk 124 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 162 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
B 167 HIS
C 167 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.155652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105078 restraints weight = 17046.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.22
r_work: 0.3060 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    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 = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  15672  Z= 0.114
  Angle     :  0.468   8.507  21180  Z= 0.248
  Chirality :  0.038   0.133   2372
  Planarity :  0.003   0.047   2592
  Dihedral  :  7.775  82.208   2116
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.45 %
    Favored  : 80.70 %
  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:  3.08 (0.20), residues: 1812
  helix:  3.02 (0.15), residues: 1148
  sheet:  1.74 (0.32), residues: 200
  loop : -0.47 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 212 
 TYR   0.013   0.001   TYR D 486 
 PHE   0.013   0.001   PHE D 502 
 TRP   0.007   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (15664)
  covalent geometry    : angle       0.46782 (21164)
  SS BOND              : bond        0.00043 (    8)
  SS BOND              : angle       0.25884 (   16)
  hydrogen bonds       : bond        0.04055 ( 1081)
  hydrogen bonds       : angle       3.96765 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 175
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7178 (mp)
REVERT: A  159 ILE cc_start: 0.8599 (mt) cc_final: 0.8273 (mm)
REVERT: A  184 ASN cc_start: 0.7445 (t0) cc_final: 0.7096 (t0)
REVERT: A  266 ASP cc_start: 0.7737 (m-30) cc_final: 0.7151 (t70)
REVERT: A  372 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6713 (mt)
REVERT: A  410 MET cc_start: 0.7825 (mtm) cc_final: 0.7376 (mtp)
REVERT: A  471 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: B   46 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7658 (mtmt)
REVERT: B  159 ILE cc_start: 0.8617 (mt) cc_final: 0.8294 (mm)
REVERT: B  217 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8091 (mtp180)
REVERT: B  231 ASP cc_start: 0.7482 (p0) cc_final: 0.6978 (t0)
REVERT: B  266 ASP cc_start: 0.7743 (m-30) cc_final: 0.7110 (t70)
REVERT: B  300 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7180 (mt)
REVERT: B  410 MET cc_start: 0.7818 (mtm) cc_final: 0.7367 (mtp)
REVERT: B  471 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: C   60 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7404 (tpp-160)
REVERT: C   87 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6883 (p0)
REVERT: C  159 ILE cc_start: 0.8613 (mt) cc_final: 0.8289 (mm)
REVERT: C  184 ASN cc_start: 0.7816 (t0) cc_final: 0.7450 (m-40)
REVERT: C  217 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8076 (mtp180)
REVERT: C  266 ASP cc_start: 0.7733 (m-30) cc_final: 0.7096 (t70)
REVERT: C  300 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7204 (mt)
REVERT: C  410 MET cc_start: 0.7779 (mtm) cc_final: 0.7362 (mtp)
REVERT: C  471 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: D   45 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6995 (mp)
REVERT: D   60 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7419 (tpp-160)
REVERT: D  159 ILE cc_start: 0.8611 (mt) cc_final: 0.8279 (mm)
REVERT: D  184 ASN cc_start: 0.7388 (t0) cc_final: 0.6961 (m-40)
REVERT: D  217 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8083 (mtp180)
REVERT: D  266 ASP cc_start: 0.7745 (m-30) cc_final: 0.7114 (t70)
REVERT: D  273 GLU cc_start: 0.7640 (pm20) cc_final: 0.7430 (pm20)
REVERT: D  410 MET cc_start: 0.7830 (mtm) cc_final: 0.7372 (mtp)
REVERT: D  471 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7935 (tt0)
  outliers start: 48
  outliers final: 29
  residues processed: 213
  average time/residue: 0.4928
  time to fit residues: 118.8063
Evaluate side-chains
  209 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  447 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  217 ARG
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  395 ARG
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  513 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 123 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 115 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 162 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 153 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 167 HIS
C 167 HIS
D 167 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.152411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101613 restraints weight = 16988.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 2.21
r_work: 0.3009 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15672  Z= 0.159
  Angle     :  0.532   8.577  21180  Z= 0.277
  Chirality :  0.040   0.138   2372
  Planarity :  0.003   0.046   2592
  Dihedral  :  7.886  79.854   2116
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.52 %
    Favored  : 79.93 %
  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:  2.95 (0.20), residues: 1812
  helix:  2.90 (0.15), residues: 1148
  sheet:  1.75 (0.32), residues: 200
  loop : -0.50 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.015   0.001   TYR D 486 
 PHE   0.011   0.001   PHE C 420 
 TRP   0.008   0.001   TRP C 390 
 HIS   0.003   0.001   HIS C 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (15664)
  covalent geometry    : angle       0.53169 (21164)
  SS BOND              : bond        0.00067 (    8)
  SS BOND              : angle       0.24067 (   16)
  hydrogen bonds       : bond        0.04729 ( 1081)
  hydrogen bonds       : angle       4.14344 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7203 (mp)
REVERT: A  159 ILE cc_start: 0.8619 (mt) cc_final: 0.8315 (mm)
REVERT: A  184 ASN cc_start: 0.7437 (t0) cc_final: 0.7100 (t0)
REVERT: A  266 ASP cc_start: 0.7813 (m-30) cc_final: 0.7229 (t70)
REVERT: A  372 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6806 (mt)
REVERT: A  410 MET cc_start: 0.7888 (mtm) cc_final: 0.7436 (mtp)
REVERT: A  471 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7806 (mt0)
REVERT: B  159 ILE cc_start: 0.8677 (mt) cc_final: 0.8339 (mm)
REVERT: B  184 ASN cc_start: 0.7811 (t0) cc_final: 0.7466 (m-40)
REVERT: B  217 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8093 (mtp180)
REVERT: B  266 ASP cc_start: 0.7778 (m-30) cc_final: 0.7172 (t70)
REVERT: B  273 GLU cc_start: 0.7649 (pm20) cc_final: 0.7419 (pm20)
REVERT: B  410 MET cc_start: 0.7836 (mtm) cc_final: 0.7432 (mtp)
REVERT: B  471 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7811 (mt0)
REVERT: C   60 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7417 (tpp-160)
REVERT: C   87 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.7005 (p0)
REVERT: C  159 ILE cc_start: 0.8690 (mt) cc_final: 0.8332 (mm)
REVERT: C  184 ASN cc_start: 0.7886 (t0) cc_final: 0.7563 (m-40)
REVERT: C  217 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8101 (mtp180)
REVERT: C  266 ASP cc_start: 0.7769 (m-30) cc_final: 0.7159 (t70)
REVERT: C  410 MET cc_start: 0.7827 (mtm) cc_final: 0.7406 (mtp)
REVERT: C  471 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7796 (mt0)
REVERT: D   45 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7097 (mp)
REVERT: D   60 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7413 (tpp-160)
REVERT: D  159 ILE cc_start: 0.8678 (mt) cc_final: 0.8341 (mm)
REVERT: D  184 ASN cc_start: 0.7474 (t0) cc_final: 0.7135 (m-40)
REVERT: D  217 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8121 (mtp180)
REVERT: D  238 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6058 (tpp-160)
REVERT: D  266 ASP cc_start: 0.7826 (m-30) cc_final: 0.7251 (t70)
REVERT: D  410 MET cc_start: 0.7825 (mtm) cc_final: 0.7406 (mtp)
REVERT: D  471 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7955 (tt0)
  outliers start: 43
  outliers final: 31
  residues processed: 206
  average time/residue: 0.5250
  time to fit residues: 121.7009
Evaluate side-chains
  209 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ARG
Chi-restraints excluded: chain A residue  447 GLU
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  447 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  447 GLU
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  217 ARG
Chi-restraints excluded: chain D residue  238 ARG
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  513 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 162 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 119 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 120 optimal weight:    0.0670
   chunk 114 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 157 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    2.1724

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.150412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.098970 restraints weight = 17051.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.24
r_work: 0.2971 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  15672  Z= 0.230
  Angle     :  0.585   8.850  21180  Z= 0.306
  Chirality :  0.042   0.148   2372
  Planarity :  0.003   0.044   2592
  Dihedral  :  8.337  76.636   2116
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.86 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.70 (0.20), residues: 1812
  helix:  2.68 (0.15), residues: 1148
  sheet:  1.74 (0.32), residues: 200
  loop : -0.56 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.017   0.002   TYR D 486 
 PHE   0.014   0.002   PHE D 420 
 TRP   0.008   0.001   TRP C 390 
 HIS   0.003   0.001   HIS D 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (15664)
  covalent geometry    : angle       0.58547 (21164)
  SS BOND              : bond        0.00119 (    8)
  SS BOND              : angle       0.37142 (   16)
  hydrogen bonds       : bond        0.05474 ( 1081)
  hydrogen bonds       : angle       4.36243 ( 3447)

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 180
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 ILE cc_start: 0.8648 (mt) cc_final: 0.8300 (mm)
REVERT: A  184 ASN cc_start: 0.7508 (t0) cc_final: 0.7129 (t0)
REVERT: A  238 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5998 (tpp-160)
REVERT: A  266 ASP cc_start: 0.7852 (m-30) cc_final: 0.7266 (t70)
REVERT: A  372 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6762 (mt)
REVERT: A  410 MET cc_start: 0.7918 (mtm) cc_final: 0.7444 (mtp)
REVERT: A  471 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7867 (mt0)
REVERT: B  159 ILE cc_start: 0.8716 (mt) cc_final: 0.8362 (mm)
REVERT: B  184 ASN cc_start: 0.7797 (t0) cc_final: 0.7546 (m-40)
REVERT: B  217 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8074 (mtp180)
REVERT: B  266 ASP cc_start: 0.7840 (m-30) cc_final: 0.7253 (t70)
REVERT: B  410 MET cc_start: 0.7899 (mtm) cc_final: 0.7408 (mtp)
REVERT: B  471 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7872 (mt0)
REVERT: C   60 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7458 (tpp-160)
REVERT: C  159 ILE cc_start: 0.8713 (mt) cc_final: 0.8347 (mm)
REVERT: C  184 ASN cc_start: 0.7813 (t0) cc_final: 0.7573 (m-40)
REVERT: C  217 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8077 (mtp180)
REVERT: C  238 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5957 (tpp-160)
REVERT: C  266 ASP cc_start: 0.7846 (m-30) cc_final: 0.7260 (t70)
REVERT: C  410 MET cc_start: 0.7889 (mtm) cc_final: 0.7414 (mtp)
REVERT: C  471 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7870 (mt0)
REVERT: D   45 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7257 (mp)
REVERT: D   60 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7428 (tpp-160)
REVERT: D  159 ILE cc_start: 0.8712 (mt) cc_final: 0.8349 (mm)
REVERT: D  184 ASN cc_start: 0.7519 (t0) cc_final: 0.7173 (t0)
REVERT: D  217 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8076 (mtp180)
REVERT: D  238 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5971 (tpp-160)
REVERT: D  266 ASP cc_start: 0.7860 (m-30) cc_final: 0.7278 (t70)
REVERT: D  410 MET cc_start: 0.7934 (mtm) cc_final: 0.7441 (mtp)
REVERT: D  471 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8003 (tt0)
  outliers start: 47
  outliers final: 29
  residues processed: 214
  average time/residue: 0.5891
  time to fit residues: 140.2920
Evaluate side-chains
  214 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  395 ARG
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  395 ARG
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  238 ARG
Chi-restraints excluded: chain C residue  300 ILE
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  389 VAL
Chi-restraints excluded: chain C residue  395 ARG
Chi-restraints excluded: chain C residue  511 ASP
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  217 ARG
Chi-restraints excluded: chain D residue  238 ARG
Chi-restraints excluded: chain D residue  300 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  389 VAL
Chi-restraints excluded: chain D residue  447 GLU
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  513 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 132 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 170 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
A 411 GLN
B 411 GLN
C 411 GLN
D 411 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.153147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.102831 restraints weight = 16995.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.21
r_work: 0.3028 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15672  Z= 0.130
  Angle     :  0.502   8.850  21180  Z= 0.265
  Chirality :  0.039   0.133   2372
  Planarity :  0.003   0.046   2592
  Dihedral  :  7.903  79.503   2116
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.16 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.20), residues: 1812
  helix:  2.88 (0.15), residues: 1148
  sheet:  1.62 (0.32), residues: 200
  loop : -0.57 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 212 
 TYR   0.014   0.001   TYR D 486 
 PHE   0.013   0.001   PHE C 420 
 TRP   0.008   0.001   TRP A  64 
 HIS   0.002   0.001   HIS C 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (15664)
  covalent geometry    : angle       0.50185 (21164)
  SS BOND              : bond        0.00055 (    8)
  SS BOND              : angle       0.18777 (   16)
  hydrogen bonds       : bond        0.04388 ( 1081)
  hydrogen bonds       : angle       4.09968 ( 3447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6216.16 seconds
wall clock time: 106 minutes 40.95 seconds (6400.95 seconds total)