Starting phenix.real_space_refine
on Wed Feb  4 12:11:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e4h_47510/02_2026/9e4h_47510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e4h_47510/02_2026/9e4h_47510.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/9e4h_47510/02_2026/9e4h_47510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e4h_47510/02_2026/9e4h_47510.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e4h_47510/02_2026/9e4h_47510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e4h_47510/02_2026/9e4h_47510.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=   0.014
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      87      5.16       5
     C    6588      2.51       5
     N    1686      2.21       5
     O    1926      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10287
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3429
          Classifications: {'peptide': 427}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.58, per 1000 atoms: 0.25
  Number of scatterers: 10287
  At special positions: 0
  Unit cell: (92.29, 97.324, 134.24, 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      87     16.00
     O    1926      8.00
     N    1686      7.00
     C    6588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 290 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 310 " - pdb=" SG  CYS A 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 314 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 325 " - pdb=" SG  CYS A 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  93 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 172 " - pdb=" SG  CYS C 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 290 " - pdb=" SG  CYS B 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 290 " - pdb=" SG  CYS C 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 310 " - pdb=" SG  CYS B 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 310 " - pdb=" SG  CYS C 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 314 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 314 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 323 " - pdb=" SG  CYS B 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 323 " - pdb=" SG  CYS C 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 325 " - pdb=" SG  CYS B 337 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 325 " - pdb=" SG  CYS C 337 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 495.8 milliseconds
  

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2406

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 15 sheets defined
      42.7% alpha, 26.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 70
      removed outlier: 3.755A  pdb=" N   LEU A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   VAL A  60 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.577A  pdb=" N   ALA A 130 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 142
      removed outlier: 3.749A  pdb=" N   ILE A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASP A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 162
    Processing helix  chain 'A' and resid 164 through 168
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 225 through 229
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 306 through 324
    Processing helix  chain 'A' and resid 338 through 345
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 386 through 394
    Processing helix  chain 'A' and resid 397 through 404
      removed outlier: 3.741A  pdb=" N   GLY A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU A 403 " --> pdb=" O   GLN A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 443
    Processing helix  chain 'A' and resid 446 through 465
      removed outlier: 3.598A  pdb=" N   TYR A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 70
      removed outlier: 3.755A  pdb=" N   LEU B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   VAL B  60 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.577A  pdb=" N   ALA B 130 " --> pdb=" O   THR B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 142
      removed outlier: 3.749A  pdb=" N   ILE B 137 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASP B 140 " --> pdb=" O   GLU B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 162
    Processing helix  chain 'B' and resid 164 through 168
    Processing helix  chain 'B' and resid 180 through 182
      No H-bonds generated for 'chain 'B' and resid 180 through 182'
    Processing helix  chain 'B' and resid 213 through 216
    Processing helix  chain 'B' and resid 225 through 229
    Processing helix  chain 'B' and resid 257 through 262
    Processing helix  chain 'B' and resid 306 through 324
    Processing helix  chain 'B' and resid 338 through 345
    Processing helix  chain 'B' and resid 345 through 355
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 397 through 404
      removed outlier: 3.742A  pdb=" N   GLY B 402 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU B 403 " --> pdb=" O   GLN B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 443
    Processing helix  chain 'B' and resid 446 through 465
      removed outlier: 3.598A  pdb=" N   TYR B 458 " --> pdb=" O   PHE B 454 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 70
      removed outlier: 3.755A  pdb=" N   LEU C  57 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   VAL C  60 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 126 through 130
      removed outlier: 3.577A  pdb=" N   ALA C 130 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 142
      removed outlier: 3.749A  pdb=" N   ILE C 137 " --> pdb=" O   LYS C 133 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASP C 140 " --> pdb=" O   GLU C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 162
    Processing helix  chain 'C' and resid 164 through 168
    Processing helix  chain 'C' and resid 180 through 182
      No H-bonds generated for 'chain 'C' and resid 180 through 182'
    Processing helix  chain 'C' and resid 213 through 216
    Processing helix  chain 'C' and resid 225 through 229
    Processing helix  chain 'C' and resid 257 through 262
    Processing helix  chain 'C' and resid 306 through 324
    Processing helix  chain 'C' and resid 338 through 345
    Processing helix  chain 'C' and resid 345 through 355
    Processing helix  chain 'C' and resid 386 through 394
    Processing helix  chain 'C' and resid 397 through 404
      removed outlier: 3.742A  pdb=" N   GLY C 402 " --> pdb=" O   GLU C 398 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU C 403 " --> pdb=" O   GLN C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 427 through 443
    Processing helix  chain 'C' and resid 446 through 465
      removed outlier: 3.598A  pdb=" N   TYR C 458 " --> pdb=" O   PHE C 454 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80
      removed outlier: 5.881A  pdb=" N   ASP A 223 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   LEU A 169 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 80
      removed outlier: 6.165A  pdb=" N   PHE A 269 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   ASP A 409 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   THR A 271 " --> pdb=" O   ASP A 409 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   PHE A 411 " --> pdb=" O   THR A 271 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   VAL A 273 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLU A 413 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   CYS A 275 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU A 415 " --> pdb=" O   CYS A 275 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   GLU A 277 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   TYR A 417 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ARG A 279 " --> pdb=" O   TYR A 417 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   THR A 419 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ILE A 281 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   GLU A 421 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189
      removed outlier: 6.983A  pdb=" N   LYS A 193 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ASN A  94 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291
    Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 80
      removed outlier: 5.881A  pdb=" N   ASP B 223 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   LEU B 169 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 80
      removed outlier: 6.165A  pdb=" N   PHE B 269 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   ASP B 409 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   THR B 271 " --> pdb=" O   ASP B 409 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   PHE B 411 " --> pdb=" O   THR B 271 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   VAL B 273 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLU B 413 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   CYS B 275 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU B 415 " --> pdb=" O   CYS B 275 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   GLU B 277 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   TYR B 417 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   ARG B 279 " --> pdb=" O   TYR B 417 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   THR B 419 " --> pdb=" O   ARG B 279 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ILE B 281 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   GLU B 421 " --> pdb=" O   ILE B 281 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86
    Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 189
      removed outlier: 6.983A  pdb=" N   LYS B 193 " --> pdb=" O   ASN B  94 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ASN B  94 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 290 through 291
    Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 80
      removed outlier: 5.881A  pdb=" N   ASP C 223 " --> pdb=" O   LEU C 169 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   LEU C 169 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 73 through 80
      removed outlier: 6.165A  pdb=" N   PHE C 269 " --> pdb=" O   VAL C 407 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   ASP C 409 " --> pdb=" O   PHE C 269 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   THR C 271 " --> pdb=" O   ASP C 409 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   PHE C 411 " --> pdb=" O   THR C 271 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   VAL C 273 " --> pdb=" O   PHE C 411 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLU C 413 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   CYS C 275 " --> pdb=" O   GLU C 413 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU C 415 " --> pdb=" O   CYS C 275 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   GLU C 277 " --> pdb=" O   LEU C 415 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   TYR C 417 " --> pdb=" O   GLU C 277 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   ARG C 279 " --> pdb=" O   TYR C 417 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   THR C 419 " --> pdb=" O   ARG C 279 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ILE C 281 " --> pdb=" O   THR C 419 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   GLU C 421 " --> pdb=" O   ILE C 281 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86
    Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 189
      removed outlier: 6.983A  pdb=" N   LYS C 193 " --> pdb=" O   ASN C  94 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ASN C  94 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 290 through 291

    520 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3339
        1.35 -     1.47: 2507
        1.47 -     1.58: 4561
        1.58 -     1.70: 0
        1.70 -     1.82: 120
  Bond restraints: 10527
  Sorted by residual:
  bond pdb=" CA  VAL C 103 "
       pdb=" CB  VAL C 103 "
    ideal  model  delta    sigma   weight residual
    1.534  1.543 -0.009 1.22e-02 6.72e+03 5.73e-01
  bond pdb=" N   CYS B 323 "
       pdb=" CA  CYS B 323 "
    ideal  model  delta    sigma   weight residual
    1.458  1.466 -0.008 1.08e-02 8.57e+03 4.99e-01
  bond pdb=" N   CYS A 323 "
       pdb=" CA  CYS A 323 "
    ideal  model  delta    sigma   weight residual
    1.458  1.466 -0.008 1.08e-02 8.57e+03 4.86e-01
  bond pdb=" CA  VAL B 103 "
       pdb=" CB  VAL B 103 "
    ideal  model  delta    sigma   weight residual
    1.534  1.543 -0.008 1.22e-02 6.72e+03 4.84e-01
  bond pdb=" N   CYS C 323 "
       pdb=" CA  CYS C 323 "
    ideal  model  delta    sigma   weight residual
    1.458  1.466 -0.007 1.08e-02 8.57e+03 4.70e-01
  ... (remaining 10522 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 13539
        0.95 -     1.91: 567
        1.91 -     2.86: 73
        2.86 -     3.81: 41
        3.81 -     4.77: 12
  Bond angle restraints: 14232
  Sorted by residual:
  angle pdb=" CA  CYS A 172 "
        pdb=" CB  CYS A 172 "
        pdb=" SG  CYS A 172 "
      ideal   model   delta    sigma   weight residual
     114.40  119.07   -4.67 2.30e+00 1.89e-01 4.12e+00
  angle pdb=" CA  CYS B 172 "
        pdb=" CB  CYS B 172 "
        pdb=" SG  CYS B 172 "
      ideal   model   delta    sigma   weight residual
     114.40  119.07   -4.67 2.30e+00 1.89e-01 4.11e+00
  angle pdb=" CA  CYS C 172 "
        pdb=" CB  CYS C 172 "
        pdb=" SG  CYS C 172 "
      ideal   model   delta    sigma   weight residual
     114.40  119.03   -4.63 2.30e+00 1.89e-01 4.05e+00
  angle pdb=" C   ASN C 322 "
        pdb=" N   CYS C 323 "
        pdb=" CA  CYS C 323 "
      ideal   model   delta    sigma   weight residual
     122.14  119.00    3.14 1.67e+00 3.59e-01 3.54e+00
  angle pdb=" C   ASN A 322 "
        pdb=" N   CYS A 323 "
        pdb=" CA  CYS A 323 "
      ideal   model   delta    sigma   weight residual
     122.14  119.04    3.10 1.67e+00 3.59e-01 3.44e+00
  ... (remaining 14227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 5651
       14.86 -    29.72: 490
       29.72 -    44.58: 162
       44.58 -    59.44: 57
       59.44 -    74.29: 15
  Dihedral angle restraints: 6375
    sinusoidal: 2625
      harmonic: 3750
  Sorted by residual:
  dihedral pdb=" CB  CYS C 314 "
           pdb=" SG  CYS C 314 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.17   37.83     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CB  CYS B 314 "
           pdb=" SG  CYS B 314 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.19   37.81     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CB  CYS A 314 "
           pdb=" SG  CYS A 314 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.21   37.79     1      1.00e+01 1.00e-02 2.01e+01
  ... (remaining 6372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 964
       0.028 -    0.055: 386
       0.055 -    0.083: 124
       0.083 -    0.110: 45
       0.110 -    0.138: 14
  Chirality restraints: 1533
  Sorted by residual:
  chirality pdb=" CA  ILE A 420 "
            pdb=" N   ILE A 420 "
            pdb=" C   ILE A 420 "
            pdb=" CB  ILE A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ILE C 420 "
            pdb=" N   ILE C 420 "
            pdb=" C   ILE C 420 "
            pdb=" CB  ILE C 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE B 420 "
            pdb=" N   ILE B 420 "
            pdb=" C   ILE B 420 "
            pdb=" CB  ILE B 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 1530 not shown)

  Planarity restraints: 1848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 284 "    0.017 5.00e-02 4.00e+02   2.57e-02 1.05e+00
        pdb=" N   PRO A 285 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 285 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 285 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 284 "    0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO B 285 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 285 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 285 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 284 "   -0.017 5.00e-02 4.00e+02   2.52e-02 1.02e+00
        pdb=" N   PRO C 285 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO C 285 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 285 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1845 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2572
        2.79 -     3.32: 9772
        3.32 -     3.85: 17478
        3.85 -     4.37: 21430
        4.37 -     4.90: 35906
  Nonbonded interactions: 87158
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 240 "
            pdb=" OE1 GLU C 242 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER B 240 "
            pdb=" OE1 GLU B 242 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER A 240 "
            pdb=" OE1 GLU A 242 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   TYR C 318 "
            pdb=" ND2 ASN C 322 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   TYR B 318 "
            pdb=" ND2 ASN B 322 "
     model   vdw
     2.274 3.120
  ... (remaining 87153 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.360
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.100
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:6.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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      :  0.002   0.017  10548  Z= 0.098
  Angle     :  0.483   4.766  14274  Z= 0.270
  Chirality :  0.036   0.138   1533
  Planarity :  0.002   0.026   1848
  Dihedral  : 13.484  74.294   3906
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.24), residues: 1275
  helix:  0.94 (0.26), residues: 426
  sheet: -0.14 (0.30), residues: 294
  loop :  0.89 (0.28), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 206 
 TYR   0.008   0.001   TYR C 417 
 PHE   0.008   0.001   PHE B 263 
 TRP   0.005   0.001   TRP A 233 
 HIS   0.002   0.000   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (10527)
  covalent geometry    : angle       0.47809 (14232)
  SS BOND              : bond        0.00211 (   21)
  SS BOND              : angle       1.34301 (   42)
  hydrogen bonds       : bond        0.21641 (  496)
  hydrogen bonds       : angle       9.41307 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8154 (tt0) cc_final: 0.7788 (tm-30)
REVERT: A  129 MET cc_start: 0.8297 (tpp) cc_final: 0.8070 (tpp)
REVERT: A  133 LYS cc_start: 0.9242 (tppt) cc_final: 0.8891 (tppt)
REVERT: A  136 GLU cc_start: 0.8596 (tt0) cc_final: 0.8106 (tm-30)
REVERT: A  137 ILE cc_start: 0.8542 (pt) cc_final: 0.8083 (pp)
REVERT: A  279 ARG cc_start: 0.8257 (tpp80) cc_final: 0.7858 (tpp80)
REVERT: A  340 GLU cc_start: 0.8324 (tp30) cc_final: 0.8097 (mp0)
REVERT: A  380 LYS cc_start: 0.8306 (tttp) cc_final: 0.8062 (tttt)
REVERT: A  438 GLN cc_start: 0.7978 (pt0) cc_final: 0.7639 (pt0)
REVERT: B   63 GLU cc_start: 0.8046 (tt0) cc_final: 0.7670 (tm-30)
REVERT: B  129 MET cc_start: 0.8349 (tpp) cc_final: 0.7739 (tpp)
REVERT: B  133 LYS cc_start: 0.9213 (tppt) cc_final: 0.8859 (tppt)
REVERT: B  136 GLU cc_start: 0.8512 (tt0) cc_final: 0.8125 (tm-30)
REVERT: B  137 ILE cc_start: 0.8588 (pt) cc_final: 0.8311 (pp)
REVERT: B  210 MET cc_start: 0.8550 (mpp) cc_final: 0.8191 (mpp)
REVERT: B  279 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7785 (tpp80)
REVERT: B  380 LYS cc_start: 0.8284 (tttp) cc_final: 0.7796 (ttmm)
REVERT: B  426 TYR cc_start: 0.7790 (t80) cc_final: 0.7562 (t80)
REVERT: C  124 ILE cc_start: 0.8553 (mm) cc_final: 0.8310 (mm)
REVERT: C  129 MET cc_start: 0.8344 (tpp) cc_final: 0.7310 (tpp)
REVERT: C  133 LYS cc_start: 0.9234 (tppt) cc_final: 0.8872 (tppt)
REVERT: C  136 GLU cc_start: 0.8549 (tt0) cc_final: 0.8120 (tm-30)
REVERT: C  137 ILE cc_start: 0.8579 (pt) cc_final: 0.8096 (pp)
REVERT: C  340 GLU cc_start: 0.8249 (tp30) cc_final: 0.7961 (mp0)
REVERT: C  358 GLN cc_start: 0.8527 (mt0) cc_final: 0.8181 (mt0)
REVERT: C  426 TYR cc_start: 0.7906 (t80) cc_final: 0.7611 (t80)
REVERT: C  438 GLN cc_start: 0.7905 (pt0) cc_final: 0.7466 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.7997
  time to fit residues: 172.8854
Evaluate side-chains
  106 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.0470
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 416 ASN
B  66 GLN
B 358 GLN
B 416 ASN
C  66 GLN
C 416 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.075174 restraints weight = 16160.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.68
r_work: 0.2940 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10548  Z= 0.179
  Angle     :  0.633   7.550  14274  Z= 0.323
  Chirality :  0.042   0.152   1533
  Planarity :  0.004   0.037   1848
  Dihedral  :  4.415  17.929   1398
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.89 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.24), residues: 1275
  helix:  0.84 (0.25), residues: 468
  sheet: -0.22 (0.29), residues: 270
  loop :  0.99 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 121 
 TYR   0.015   0.002   TYR B 342 
 PHE   0.011   0.001   PHE B 257 
 TRP   0.006   0.001   TRP B 233 
 HIS   0.002   0.001   HIS C 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10527)
  covalent geometry    : angle       0.62555 (14232)
  SS BOND              : bond        0.00420 (   21)
  SS BOND              : angle       1.92503 (   42)
  hydrogen bonds       : bond        0.03726 (  496)
  hydrogen bonds       : angle       6.56684 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8219 (tt0) cc_final: 0.7872 (tm-30)
REVERT: A   70 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8883 (m-70)
REVERT: A  133 LYS cc_start: 0.9313 (tppt) cc_final: 0.8933 (tppt)
REVERT: A  136 GLU cc_start: 0.8832 (tt0) cc_final: 0.8135 (tm-30)
REVERT: A  137 ILE cc_start: 0.8542 (pt) cc_final: 0.8211 (pp)
REVERT: A  235 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (tp30)
REVERT: A  279 ARG cc_start: 0.8512 (tpp80) cc_final: 0.8252 (tpp80)
REVERT: A  340 GLU cc_start: 0.8495 (tp30) cc_final: 0.8272 (mp0)
REVERT: A  380 LYS cc_start: 0.8458 (tttp) cc_final: 0.8187 (tttt)
REVERT: B   63 GLU cc_start: 0.8198 (tt0) cc_final: 0.7855 (tm-30)
REVERT: B  133 LYS cc_start: 0.9304 (tppt) cc_final: 0.8876 (tppt)
REVERT: B  136 GLU cc_start: 0.8755 (tt0) cc_final: 0.8247 (tm-30)
REVERT: B  137 ILE cc_start: 0.8587 (pt) cc_final: 0.8287 (pp)
REVERT: B  279 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8260 (tpp80)
REVERT: B  380 LYS cc_start: 0.8438 (tttp) cc_final: 0.7923 (ttmm)
REVERT: C   63 GLU cc_start: 0.8410 (tt0) cc_final: 0.7985 (tm-30)
REVERT: C  107 ASP cc_start: 0.8555 (m-30) cc_final: 0.8294 (m-30)
REVERT: C  133 LYS cc_start: 0.9302 (tppt) cc_final: 0.8861 (tppt)
REVERT: C  136 GLU cc_start: 0.8699 (tt0) cc_final: 0.8136 (tm-30)
REVERT: C  137 ILE cc_start: 0.8546 (pt) cc_final: 0.8140 (pp)
  outliers start: 24
  outliers final: 10
  residues processed: 140
  average time/residue: 0.6778
  time to fit residues: 101.1039
Evaluate side-chains
  112 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  392 LYS
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  376 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9980
   chunk 120 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
C 216 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.105300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.074378 restraints weight = 16253.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 2.70
r_work: 0.2927 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10548  Z= 0.148
  Angle     :  0.583  10.843  14274  Z= 0.292
  Chirality :  0.040   0.172   1533
  Planarity :  0.003   0.034   1848
  Dihedral  :  4.495  20.868   1398
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.10 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.24), residues: 1275
  helix:  0.98 (0.25), residues: 468
  sheet: -0.32 (0.29), residues: 270
  loop :  0.88 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 121 
 TYR   0.011   0.001   TYR B 342 
 PHE   0.008   0.001   PHE B 152 
 TRP   0.006   0.001   TRP B  46 
 HIS   0.002   0.000   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10527)
  covalent geometry    : angle       0.57387 (14232)
  SS BOND              : bond        0.00540 (   21)
  SS BOND              : angle       1.98128 (   42)
  hydrogen bonds       : bond        0.03292 (  496)
  hydrogen bonds       : angle       5.82672 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8181 (tt0) cc_final: 0.7874 (tm-30)
REVERT: A   70 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8878 (m-70)
REVERT: A  133 LYS cc_start: 0.9304 (tppt) cc_final: 0.8904 (tppt)
REVERT: A  136 GLU cc_start: 0.8772 (tt0) cc_final: 0.8100 (tm-30)
REVERT: A  137 ILE cc_start: 0.8581 (pt) cc_final: 0.8310 (pp)
REVERT: A  279 ARG cc_start: 0.8463 (tpp80) cc_final: 0.8247 (tpp80)
REVERT: A  340 GLU cc_start: 0.8530 (tp30) cc_final: 0.8216 (mp0)
REVERT: A  359 GLU cc_start: 0.8858 (pt0) cc_final: 0.8601 (pp20)
REVERT: A  380 LYS cc_start: 0.8518 (tttp) cc_final: 0.8255 (tttt)
REVERT: A  392 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8943 (tttm)
REVERT: B   63 GLU cc_start: 0.8214 (tt0) cc_final: 0.7812 (tm-30)
REVERT: B  104 SER cc_start: 0.8890 (t) cc_final: 0.8559 (p)
REVERT: B  133 LYS cc_start: 0.9306 (tppt) cc_final: 0.8852 (tppt)
REVERT: B  136 GLU cc_start: 0.8753 (tt0) cc_final: 0.8213 (tm-30)
REVERT: B  137 ILE cc_start: 0.8602 (pt) cc_final: 0.8297 (pp)
REVERT: B  154 MET cc_start: 0.8716 (tpt) cc_final: 0.8501 (tpt)
REVERT: B  279 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8302 (tpp80)
REVERT: B  359 GLU cc_start: 0.8962 (pt0) cc_final: 0.8697 (pp20)
REVERT: B  380 LYS cc_start: 0.8472 (tttp) cc_final: 0.7952 (ttmm)
REVERT: B  426 TYR cc_start: 0.8044 (t80) cc_final: 0.7521 (t80)
REVERT: C   63 GLU cc_start: 0.8326 (tt0) cc_final: 0.7907 (tm-30)
REVERT: C  107 ASP cc_start: 0.8620 (m-30) cc_final: 0.8325 (m-30)
REVERT: C  133 LYS cc_start: 0.9294 (tppt) cc_final: 0.8837 (tppt)
REVERT: C  136 GLU cc_start: 0.8666 (tt0) cc_final: 0.8098 (tm-30)
REVERT: C  137 ILE cc_start: 0.8598 (pt) cc_final: 0.8143 (pp)
  outliers start: 30
  outliers final: 12
  residues processed: 133
  average time/residue: 0.6670
  time to fit residues: 94.3845
Evaluate side-chains
  121 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  392 LYS
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  216 ASN
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  376 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B  66 GLN
C  66 GLN
C 216 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.101551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.070058 restraints weight = 16312.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.72
r_work: 0.2845 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10548  Z= 0.277
  Angle     :  0.682  10.893  14274  Z= 0.344
  Chirality :  0.043   0.185   1533
  Planarity :  0.004   0.031   1848
  Dihedral  :  4.919  23.289   1398
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 13.81 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.24), residues: 1275
  helix:  1.07 (0.26), residues: 465
  sheet: -0.50 (0.29), residues: 270
  loop :  0.65 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 166 
 TYR   0.015   0.002   TYR A 360 
 PHE   0.011   0.001   PHE C 257 
 TRP   0.006   0.001   TRP B  46 
 HIS   0.002   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 (10527)
  covalent geometry    : angle       0.66583 (14232)
  SS BOND              : bond        0.00930 (   21)
  SS BOND              : angle       2.83058 (   42)
  hydrogen bonds       : bond        0.03394 (  496)
  hydrogen bonds       : angle       5.69204 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8447 (m)
REVERT: A   63 GLU cc_start: 0.8204 (tt0) cc_final: 0.7887 (tm-30)
REVERT: A  133 LYS cc_start: 0.9295 (tppt) cc_final: 0.8872 (tppt)
REVERT: A  136 GLU cc_start: 0.8825 (tt0) cc_final: 0.8097 (tm-30)
REVERT: A  137 ILE cc_start: 0.8720 (pt) cc_final: 0.8446 (pp)
REVERT: A  279 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8251 (tpp80)
REVERT: A  340 GLU cc_start: 0.8563 (tp30) cc_final: 0.8251 (mp0)
REVERT: A  359 GLU cc_start: 0.8871 (pt0) cc_final: 0.8621 (pp20)
REVERT: A  380 LYS cc_start: 0.8625 (tttp) cc_final: 0.8404 (ttpt)
REVERT: A  392 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8977 (tttm)
REVERT: B   63 GLU cc_start: 0.8223 (tt0) cc_final: 0.7840 (tm-30)
REVERT: B  104 SER cc_start: 0.8861 (t) cc_final: 0.8538 (p)
REVERT: B  133 LYS cc_start: 0.9302 (tppt) cc_final: 0.8825 (tppt)
REVERT: B  136 GLU cc_start: 0.8846 (tt0) cc_final: 0.8258 (tm-30)
REVERT: B  279 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8285 (tpp80)
REVERT: B  295 MET cc_start: 0.3566 (pp-130) cc_final: 0.3346 (pp-130)
REVERT: B  359 GLU cc_start: 0.8989 (pt0) cc_final: 0.8710 (pp20)
REVERT: B  380 LYS cc_start: 0.8540 (tttp) cc_final: 0.8010 (ttmm)
REVERT: B  426 TYR cc_start: 0.8130 (t80) cc_final: 0.7703 (t80)
REVERT: C   63 GLU cc_start: 0.8332 (tt0) cc_final: 0.7917 (tm-30)
REVERT: C  107 ASP cc_start: 0.8783 (m-30) cc_final: 0.8510 (m-30)
REVERT: C  133 LYS cc_start: 0.9254 (tppt) cc_final: 0.8741 (tppt)
REVERT: C  136 GLU cc_start: 0.8706 (tt0) cc_final: 0.8160 (tm-30)
REVERT: C  279 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7771 (ttp-170)
  outliers start: 40
  outliers final: 15
  residues processed: 139
  average time/residue: 0.7105
  time to fit residues: 105.0394
Evaluate side-chains
  129 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  392 LYS
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  438 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0970
   chunk 92 optimal weight:    4.9990
   chunk 42 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9980
   chunk 117 optimal weight:    0.6980
   chunk 119 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A 216 ASN
B  66 GLN
C 216 ASN
C 358 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.103625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.072345 restraints weight = 16225.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.73
r_work: 0.2889 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10548  Z= 0.140
  Angle     :  0.610  10.275  14274  Z= 0.306
  Chirality :  0.040   0.164   1533
  Planarity :  0.003   0.029   1848
  Dihedral  :  4.760  24.573   1398
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.80 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.24), residues: 1275
  helix:  1.11 (0.26), residues: 468
  sheet: -0.64 (0.29), residues: 270
  loop :  0.67 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 166 
 TYR   0.012   0.001   TYR B 342 
 PHE   0.007   0.001   PHE B 263 
 TRP   0.003   0.001   TRP B 233 
 HIS   0.005   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10527)
  covalent geometry    : angle       0.59945 (14232)
  SS BOND              : bond        0.00470 (   21)
  SS BOND              : angle       2.17229 (   42)
  hydrogen bonds       : bond        0.03057 (  496)
  hydrogen bonds       : angle       5.55593 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.8172 (tt0) cc_final: 0.7866 (tm-30)
REVERT: A   70 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8897 (m-70)
REVERT: A  107 ASP cc_start: 0.8737 (m-30) cc_final: 0.8417 (m-30)
REVERT: A  133 LYS cc_start: 0.9284 (tppt) cc_final: 0.8842 (tppt)
REVERT: A  136 GLU cc_start: 0.8745 (tt0) cc_final: 0.8026 (tm-30)
REVERT: A  137 ILE cc_start: 0.8718 (pt) cc_final: 0.8449 (pp)
REVERT: A  201 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7650 (mmm160)
REVERT: A  340 GLU cc_start: 0.8570 (tp30) cc_final: 0.8268 (mp0)
REVERT: A  359 GLU cc_start: 0.8788 (pt0) cc_final: 0.8558 (pp20)
REVERT: A  380 LYS cc_start: 0.8583 (tttp) cc_final: 0.8369 (ttpt)
REVERT: A  392 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8991 (tttm)
REVERT: B   63 GLU cc_start: 0.8237 (tt0) cc_final: 0.7844 (tm-30)
REVERT: B  104 SER cc_start: 0.8894 (t) cc_final: 0.8568 (p)
REVERT: B  133 LYS cc_start: 0.9304 (tppt) cc_final: 0.8725 (tppt)
REVERT: B  136 GLU cc_start: 0.8820 (tt0) cc_final: 0.8202 (tm-30)
REVERT: B  137 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8159 (pp)
REVERT: B  295 MET cc_start: 0.3737 (pp-130) cc_final: 0.3483 (pp-130)
REVERT: B  359 GLU cc_start: 0.8873 (pt0) cc_final: 0.8569 (pp20)
REVERT: B  380 LYS cc_start: 0.8514 (tttp) cc_final: 0.8006 (ttmm)
REVERT: B  426 TYR cc_start: 0.8080 (t80) cc_final: 0.7574 (t80)
REVERT: C   63 GLU cc_start: 0.8294 (tt0) cc_final: 0.7890 (tm-30)
REVERT: C  107 ASP cc_start: 0.8782 (m-30) cc_final: 0.8458 (m-30)
REVERT: C  133 LYS cc_start: 0.9251 (tppt) cc_final: 0.8743 (tppt)
REVERT: C  136 GLU cc_start: 0.8671 (tt0) cc_final: 0.8038 (tm-30)
REVERT: C  137 ILE cc_start: 0.8774 (pt) cc_final: 0.8243 (pp)
REVERT: C  189 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8981 (p)
REVERT: C  279 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7816 (ttp-170)
  outliers start: 31
  outliers final: 14
  residues processed: 133
  average time/residue: 0.6652
  time to fit residues: 93.9944
Evaluate side-chains
  133 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  438 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 122 optimal weight:    0.8980
   chunk 125 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0270
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B  66 GLN
C 216 ASN
C 358 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.103882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.072759 restraints weight = 16354.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.74
r_work: 0.2897 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10548  Z= 0.134
  Angle     :  0.586   9.691  14274  Z= 0.293
  Chirality :  0.040   0.158   1533
  Planarity :  0.003   0.028   1848
  Dihedral  :  4.599  25.082   1398
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.40 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.24), residues: 1275
  helix:  1.39 (0.26), residues: 456
  sheet: -0.61 (0.28), residues: 282
  loop :  0.63 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 166 
 TYR   0.010   0.001   TYR C 195 
 PHE   0.008   0.001   PHE A 263 
 TRP   0.004   0.001   TRP B 233 
 HIS   0.003   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10527)
  covalent geometry    : angle       0.57703 (14232)
  SS BOND              : bond        0.00429 (   21)
  SS BOND              : angle       1.92971 (   42)
  hydrogen bonds       : bond        0.02870 (  496)
  hydrogen bonds       : angle       5.38341 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 CYS cc_start: 0.8712 (t) cc_final: 0.8433 (m)
REVERT: A   63 GLU cc_start: 0.8179 (tt0) cc_final: 0.7835 (tm-30)
REVERT: A  107 ASP cc_start: 0.8758 (m-30) cc_final: 0.8441 (m-30)
REVERT: A  133 LYS cc_start: 0.9272 (tppt) cc_final: 0.8822 (tppt)
REVERT: A  201 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7624 (mmm160)
REVERT: A  279 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8058 (tpp80)
REVERT: A  340 GLU cc_start: 0.8586 (tp30) cc_final: 0.8271 (mp0)
REVERT: A  359 GLU cc_start: 0.8715 (pt0) cc_final: 0.8498 (pp20)
REVERT: A  380 LYS cc_start: 0.8641 (tttp) cc_final: 0.8437 (ttpt)
REVERT: A  392 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8973 (tttm)
REVERT: B   63 GLU cc_start: 0.8223 (tt0) cc_final: 0.7829 (tm-30)
REVERT: B  104 SER cc_start: 0.8858 (t) cc_final: 0.8552 (p)
REVERT: B  133 LYS cc_start: 0.9299 (tppt) cc_final: 0.8788 (tppt)
REVERT: B  136 GLU cc_start: 0.8827 (tt0) cc_final: 0.8166 (tm-30)
REVERT: B  235 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7891 (mp0)
REVERT: B  279 ARG cc_start: 0.8425 (tpp80) cc_final: 0.7976 (ttp-170)
REVERT: B  359 GLU cc_start: 0.8807 (pt0) cc_final: 0.8478 (pp20)
REVERT: B  380 LYS cc_start: 0.8517 (tttp) cc_final: 0.8011 (ttmm)
REVERT: B  426 TYR cc_start: 0.8077 (t80) cc_final: 0.7638 (t80)
REVERT: C   61 CYS cc_start: 0.8644 (t) cc_final: 0.8403 (m)
REVERT: C   63 GLU cc_start: 0.8244 (tt0) cc_final: 0.7879 (tm-30)
REVERT: C  107 ASP cc_start: 0.8806 (m-30) cc_final: 0.8490 (m-30)
REVERT: C  133 LYS cc_start: 0.9246 (tppt) cc_final: 0.8727 (tppt)
REVERT: C  136 GLU cc_start: 0.8649 (tt0) cc_final: 0.8027 (tm-30)
REVERT: C  137 ILE cc_start: 0.8791 (pt) cc_final: 0.8256 (pp)
REVERT: C  189 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8966 (p)
REVERT: C  279 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7836 (ttp-170)
  outliers start: 31
  outliers final: 13
  residues processed: 131
  average time/residue: 0.6966
  time to fit residues: 96.8522
Evaluate side-chains
  131 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  376 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 63 optimal weight:    0.0060
   chunk 82 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0570
   chunk 20 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 90 optimal weight:    0.5980
   chunk 105 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.4914

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B  66 GLN
C 216 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.104296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.073319 restraints weight = 16119.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.72
r_work: 0.2910 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10548  Z= 0.127
  Angle     :  0.573   8.979  14274  Z= 0.287
  Chirality :  0.039   0.161   1533
  Planarity :  0.003   0.031   1848
  Dihedral  :  4.520  25.435   1398
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.49 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.24), residues: 1275
  helix:  1.50 (0.26), residues: 456
  sheet: -0.61 (0.28), residues: 282
  loop :  0.62 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 145 
 TYR   0.010   0.001   TYR C 195 
 PHE   0.008   0.001   PHE A 263 
 TRP   0.004   0.001   TRP C 233 
 HIS   0.003   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10527)
  covalent geometry    : angle       0.56507 (14232)
  SS BOND              : bond        0.00395 (   21)
  SS BOND              : angle       1.81182 (   42)
  hydrogen bonds       : bond        0.02795 (  496)
  hydrogen bonds       : angle       5.28832 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8429 (m)
REVERT: A   63 GLU cc_start: 0.8150 (tt0) cc_final: 0.7798 (tm-30)
REVERT: A  104 SER cc_start: 0.8736 (t) cc_final: 0.8422 (p)
REVERT: A  133 LYS cc_start: 0.9275 (tppt) cc_final: 0.8808 (tppt)
REVERT: A  279 ARG cc_start: 0.8411 (tpp80) cc_final: 0.7982 (ttp-170)
REVERT: A  340 GLU cc_start: 0.8575 (tp30) cc_final: 0.8274 (mp0)
REVERT: A  359 GLU cc_start: 0.8658 (pt0) cc_final: 0.8440 (pp20)
REVERT: A  380 LYS cc_start: 0.8637 (tttp) cc_final: 0.8427 (ttpt)
REVERT: B   63 GLU cc_start: 0.8220 (tt0) cc_final: 0.7819 (tm-30)
REVERT: B  104 SER cc_start: 0.8850 (t) cc_final: 0.8544 (p)
REVERT: B  133 LYS cc_start: 0.9294 (tppt) cc_final: 0.8775 (tppt)
REVERT: B  136 GLU cc_start: 0.8805 (tt0) cc_final: 0.8134 (tm-30)
REVERT: B  235 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7868 (mp0)
REVERT: B  279 ARG cc_start: 0.8425 (tpp80) cc_final: 0.7975 (ttp-170)
REVERT: B  359 GLU cc_start: 0.8735 (pt0) cc_final: 0.8400 (pp20)
REVERT: B  380 LYS cc_start: 0.8502 (tttp) cc_final: 0.8003 (ttmm)
REVERT: B  426 TYR cc_start: 0.8138 (t80) cc_final: 0.7681 (t80)
REVERT: C   63 GLU cc_start: 0.8233 (tt0) cc_final: 0.7830 (tm-30)
REVERT: C  107 ASP cc_start: 0.8815 (m-30) cc_final: 0.8504 (m-30)
REVERT: C  133 LYS cc_start: 0.9242 (tppt) cc_final: 0.8759 (tppt)
REVERT: C  189 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.9011 (p)
REVERT: C  279 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8010 (ttp-170)
  outliers start: 25
  outliers final: 17
  residues processed: 128
  average time/residue: 0.7584
  time to fit residues: 103.0268
Evaluate side-chains
  132 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  235 GLU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  458 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0770
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 125 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 329 HIS
C 216 ASN
C 358 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.104110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.072984 restraints weight = 16159.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 2.73
r_work: 0.2901 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10548  Z= 0.139
  Angle     :  0.584   8.643  14274  Z= 0.291
  Chirality :  0.040   0.162   1533
  Planarity :  0.003   0.039   1848
  Dihedral  :  4.530  26.457   1398
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.76 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.24), residues: 1275
  helix:  1.31 (0.26), residues: 474
  sheet: -0.63 (0.29), residues: 264
  loop :  0.58 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 201 
 TYR   0.010   0.001   TYR B 342 
 PHE   0.009   0.001   PHE A 263 
 TRP   0.005   0.000   TRP C 233 
 HIS   0.002   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10527)
  covalent geometry    : angle       0.57650 (14232)
  SS BOND              : bond        0.00411 (   21)
  SS BOND              : angle       1.80300 (   42)
  hydrogen bonds       : bond        0.02750 (  496)
  hydrogen bonds       : angle       5.18869 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 CYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8432 (m)
REVERT: A   63 GLU cc_start: 0.8164 (tt0) cc_final: 0.7802 (tm-30)
REVERT: A  104 SER cc_start: 0.8707 (t) cc_final: 0.8393 (p)
REVERT: A  133 LYS cc_start: 0.9263 (tppt) cc_final: 0.8799 (tppt)
REVERT: A  279 ARG cc_start: 0.8411 (tpp80) cc_final: 0.7979 (ttp-170)
REVERT: A  340 GLU cc_start: 0.8574 (tp30) cc_final: 0.8264 (mp0)
REVERT: A  380 LYS cc_start: 0.8638 (tttp) cc_final: 0.8434 (ttpt)
REVERT: B   63 GLU cc_start: 0.8207 (tt0) cc_final: 0.7813 (tm-30)
REVERT: B  104 SER cc_start: 0.8830 (t) cc_final: 0.8521 (p)
REVERT: B  133 LYS cc_start: 0.9280 (tppt) cc_final: 0.8753 (tppt)
REVERT: B  136 GLU cc_start: 0.8813 (tt0) cc_final: 0.8150 (tm-30)
REVERT: B  279 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8017 (ttp-170)
REVERT: B  359 GLU cc_start: 0.8734 (pt0) cc_final: 0.8467 (pp20)
REVERT: B  380 LYS cc_start: 0.8497 (tttp) cc_final: 0.8006 (ttmm)
REVERT: B  426 TYR cc_start: 0.8128 (t80) cc_final: 0.7674 (t80)
REVERT: C   63 GLU cc_start: 0.8210 (tt0) cc_final: 0.7827 (tm-30)
REVERT: C  107 ASP cc_start: 0.8766 (m-30) cc_final: 0.8437 (m-30)
REVERT: C  133 LYS cc_start: 0.9240 (tppt) cc_final: 0.9032 (mmmm)
REVERT: C  136 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8082 (tm-30)
REVERT: C  189 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9020 (p)
REVERT: C  279 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7848 (ttp-170)
REVERT: C  358 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8774 (tp40)
  outliers start: 29
  outliers final: 18
  residues processed: 131
  average time/residue: 0.7153
  time to fit residues: 99.4275
Evaluate side-chains
  132 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  137 ILE
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain C residue   58 LEU
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain C residue  358 GLN
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  458 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 120 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 97 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0870
   chunk 71 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 216 ASN
B  66 GLN
C  66 GLN
C 216 ASN
C 358 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.104572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.073491 restraints weight = 16043.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.72
r_work: 0.2910 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10548  Z= 0.125
  Angle     :  0.581   8.607  14274  Z= 0.289
  Chirality :  0.039   0.156   1533
  Planarity :  0.003   0.032   1848
  Dihedral  :  4.485  26.450   1398
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.74 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.24), residues: 1275
  helix:  1.36 (0.26), residues: 474
  sheet: -0.64 (0.29), residues: 264
  loop :  0.56 (0.28), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 145 
 TYR   0.009   0.001   TYR B 195 
 PHE   0.012   0.001   PHE A 157 
 TRP   0.007   0.001   TRP C 233 
 HIS   0.002   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10527)
  covalent geometry    : angle       0.57447 (14232)
  SS BOND              : bond        0.00368 (   21)
  SS BOND              : angle       1.70607 (   42)
  hydrogen bonds       : bond        0.02710 (  496)
  hydrogen bonds       : angle       5.14855 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   61 CYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8432 (m)
REVERT: A   63 GLU cc_start: 0.8167 (tt0) cc_final: 0.7801 (tm-30)
REVERT: A  104 SER cc_start: 0.8677 (t) cc_final: 0.8394 (p)
REVERT: A  136 GLU cc_start: 0.8677 (tt0) cc_final: 0.8155 (tm-30)
REVERT: A  279 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7958 (ttp-170)
REVERT: A  340 GLU cc_start: 0.8578 (tp30) cc_final: 0.8267 (mp0)
REVERT: A  380 LYS cc_start: 0.8620 (tttp) cc_final: 0.8408 (ttpt)
REVERT: B   63 GLU cc_start: 0.8194 (tt0) cc_final: 0.7799 (tm-30)
REVERT: B  104 SER cc_start: 0.8819 (t) cc_final: 0.8528 (p)
REVERT: B  133 LYS cc_start: 0.9280 (tppt) cc_final: 0.8766 (tppt)
REVERT: B  136 GLU cc_start: 0.8806 (tt0) cc_final: 0.8136 (tm-30)
REVERT: B  279 ARG cc_start: 0.8448 (tpp80) cc_final: 0.8016 (ttp-170)
REVERT: B  359 GLU cc_start: 0.8695 (pt0) cc_final: 0.8418 (pp20)
REVERT: B  380 LYS cc_start: 0.8492 (tttp) cc_final: 0.8009 (ttmm)
REVERT: B  426 TYR cc_start: 0.8175 (t80) cc_final: 0.7706 (t80)
REVERT: C   63 GLU cc_start: 0.8157 (tt0) cc_final: 0.7799 (tm-30)
REVERT: C  107 ASP cc_start: 0.8767 (m-30) cc_final: 0.8441 (m-30)
REVERT: C  133 LYS cc_start: 0.9242 (tppt) cc_final: 0.9031 (mmmm)
REVERT: C  136 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8042 (tm-30)
REVERT: C  189 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9025 (p)
REVERT: C  279 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8006 (ttp-170)
REVERT: C  358 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8724 (tp40)
  outliers start: 24
  outliers final: 15
  residues processed: 123
  average time/residue: 0.7340
  time to fit residues: 96.2110
Evaluate side-chains
  128 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  458 TYR
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain C residue  358 GLN
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  458 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 118 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 74 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0770
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 358 GLN
C 216 ASN
C 358 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.104686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.073713 restraints weight = 16009.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.72
r_work: 0.2915 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10548  Z= 0.126
  Angle     :  0.600  13.191  14274  Z= 0.294
  Chirality :  0.039   0.157   1533
  Planarity :  0.003   0.036   1848
  Dihedral  :  4.474  26.316   1398
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.00 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.24), residues: 1275
  helix:  1.43 (0.26), residues: 471
  sheet: -0.65 (0.29), residues: 264
  loop :  0.51 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 145 
 TYR   0.009   0.001   TYR C 360 
 PHE   0.011   0.001   PHE A 157 
 TRP   0.012   0.001   TRP C 233 
 HIS   0.002   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10527)
  covalent geometry    : angle       0.59380 (14232)
  SS BOND              : bond        0.00369 (   21)
  SS BOND              : angle       1.67777 (   42)
  hydrogen bonds       : bond        0.02685 (  496)
  hydrogen bonds       : angle       5.12096 ( 1461)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   61 CYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8415 (m)
REVERT: A   63 GLU cc_start: 0.8168 (tt0) cc_final: 0.7799 (tm-30)
REVERT: A  104 SER cc_start: 0.8684 (t) cc_final: 0.8427 (p)
REVERT: A  136 GLU cc_start: 0.8682 (tt0) cc_final: 0.8182 (tm-30)
REVERT: A  201 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7571 (mmm160)
REVERT: A  279 ARG cc_start: 0.8393 (tpp80) cc_final: 0.7949 (ttp-170)
REVERT: A  340 GLU cc_start: 0.8585 (tp30) cc_final: 0.8267 (mp0)
REVERT: A  380 LYS cc_start: 0.8616 (tttp) cc_final: 0.8402 (ttpt)
REVERT: B   63 GLU cc_start: 0.8186 (tt0) cc_final: 0.7788 (tm-30)
REVERT: B  104 SER cc_start: 0.8813 (t) cc_final: 0.8527 (p)
REVERT: B  133 LYS cc_start: 0.9285 (tppt) cc_final: 0.8766 (tppt)
REVERT: B  136 GLU cc_start: 0.8833 (tt0) cc_final: 0.8160 (tm-30)
REVERT: B  279 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7985 (ttp-170)
REVERT: B  359 GLU cc_start: 0.8667 (pt0) cc_final: 0.8445 (pp20)
REVERT: B  380 LYS cc_start: 0.8470 (tttp) cc_final: 0.7990 (ttmm)
REVERT: B  426 TYR cc_start: 0.8162 (t80) cc_final: 0.7698 (t80)
REVERT: C   63 GLU cc_start: 0.8179 (tt0) cc_final: 0.7814 (tm-30)
REVERT: C  104 SER cc_start: 0.8772 (t) cc_final: 0.8339 (p)
REVERT: C  189 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9033 (p)
REVERT: C  279 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8016 (ttp-170)
REVERT: C  345 CYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7272 (t)
REVERT: C  358 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8731 (tp40)
  outliers start: 23
  outliers final: 13
  residues processed: 123
  average time/residue: 0.7283
  time to fit residues: 95.2610
Evaluate side-chains
  129 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  458 TYR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  345 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  279 ARG
Chi-restraints excluded: chain C residue  289 THR
Chi-restraints excluded: chain C residue  345 CYS
Chi-restraints excluded: chain C residue  358 GLN
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  458 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 115 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0770
   chunk 74 optimal weight:    0.8980
   chunk 124 optimal weight:    0.2980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
C 358 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.104715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.073656 restraints weight = 16083.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.74
r_work: 0.2914 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10548  Z= 0.129
  Angle     :  0.593   8.653  14274  Z= 0.292
  Chirality :  0.039   0.155   1533
  Planarity :  0.003   0.036   1848
  Dihedral  :  4.457  26.313   1398
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.18 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.24), residues: 1275
  helix:  1.43 (0.26), residues: 471
  sheet: -0.66 (0.29), residues: 264
  loop :  0.49 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 145 
 TYR   0.009   0.001   TYR C 360 
 PHE   0.010   0.001   PHE A 157 
 TRP   0.003   0.000   TRP A 233 
 HIS   0.002   0.000   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10527)
  covalent geometry    : angle       0.58725 (14232)
  SS BOND              : bond        0.00365 (   21)
  SS BOND              : angle       1.67494 (   42)
  hydrogen bonds       : bond        0.02666 (  496)
  hydrogen bonds       : angle       5.09597 ( 1461)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4139.97 seconds
wall clock time: 71 minutes 14.29 seconds (4274.29 seconds total)