Starting phenix.real_space_refine
on Sat Aug 23 00:50:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afa_15393/08_2025/8afa_15393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afa_15393/08_2025/8afa_15393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afa_15393/08_2025/8afa_15393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afa_15393/08_2025/8afa_15393.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afa_15393/08_2025/8afa_15393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afa_15393/08_2025/8afa_15393.map"
  }
  resolution = 3.16
  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=   0.012 sd=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5944      2.51       5
     N    1454      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9008
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 2989
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 16, 'TRANS': 384}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2996
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 16, 'TRANS': 385}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2996
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 16, 'TRANS': 385}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.21
  Number of scatterers: 9008
  At special positions: 0
  Unit cell: (102.828, 106.172, 80.256, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1562      8.00
     N    1454      7.00
     C    5944      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 334.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      87.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 35
    Processing helix  chain 'A' and resid 37 through 45
    Processing helix  chain 'A' and resid 45 through 59
      removed outlier: 3.543A  pdb=" N   GLY A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 74
      removed outlier: 3.525A  pdb=" N   SER A  67 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A  69 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 110
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 143 through 151
    Processing helix  chain 'A' and resid 152 through 171
      removed outlier: 3.721A  pdb=" N   VAL A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 222
      removed outlier: 3.515A  pdb=" N   ARG A 179 " --> pdb=" O   GLU A 175 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   TYR A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ARG A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   ILE A 209 " --> pdb=" O   GLN A 205 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 248
      removed outlier: 3.632A  pdb=" N   LYS A 232 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 256
      removed outlier: 3.538A  pdb=" N   LYS A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 267
    Processing helix  chain 'A' and resid 267 through 278
      removed outlier: 3.720A  pdb=" N   MET A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 294
      removed outlier: 3.752A  pdb=" N   THR A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 313
      removed outlier: 3.654A  pdb=" N   SER A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   PHE A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      Proline residue:  A 307  - end of helix
    Processing helix  chain 'A' and resid 314 through 332
      removed outlier: 3.550A  pdb=" N   LEU A 326 " --> pdb=" O   GLY A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 3.654A  pdb=" N   VAL A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 353 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLY A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 373
      removed outlier: 4.071A  pdb=" N   ILE A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   MET A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 367 " --> pdb=" O   ALA A 363 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   MET A 368 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 393
      removed outlier: 3.821A  pdb=" N   ILE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 420
      removed outlier: 4.214A  pdb=" N   GLY A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASP A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 429
    Processing helix  chain 'B' and resid 17 through 35
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 45 through 59
      removed outlier: 3.543A  pdb=" N   GLY B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 74
      removed outlier: 3.527A  pdb=" N   SER B  67 " --> pdb=" O   ILE B  63 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL B  69 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 110
    Processing helix  chain 'B' and resid 131 through 138
    Processing helix  chain 'B' and resid 143 through 151
    Processing helix  chain 'B' and resid 152 through 171
      removed outlier: 3.722A  pdb=" N   VAL B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 222
      removed outlier: 3.516A  pdb=" N   ARG B 179 " --> pdb=" O   GLU B 175 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   TYR B 206 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ARG B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   ILE B 209 " --> pdb=" O   GLN B 205 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE B 212 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 248
      removed outlier: 3.631A  pdb=" N   LYS B 232 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 256
      removed outlier: 3.539A  pdb=" N   LYS B 254 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 267
    Processing helix  chain 'B' and resid 267 through 278
      removed outlier: 3.721A  pdb=" N   MET B 271 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 294
      removed outlier: 3.751A  pdb=" N   THR B 287 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 313
      removed outlier: 3.655A  pdb=" N   SER B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   PHE B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      Proline residue:  B 307  - end of helix
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.550A  pdb=" N   LEU B 326 " --> pdb=" O   GLY B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 355
      removed outlier: 3.655A  pdb=" N   VAL B 345 " --> pdb=" O   GLN B 341 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE B 353 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLY B 354 " --> pdb=" O   LEU B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 373
      removed outlier: 4.071A  pdb=" N   ILE B 364 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA B 367 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   MET B 368 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL B 369 " --> pdb=" O   MET B 365 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 393
      removed outlier: 3.822A  pdb=" N   ILE B 393 " --> pdb=" O   MET B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 420
      removed outlier: 4.215A  pdb=" N   GLY B 400 " --> pdb=" O   ILE B 396 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 406 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR B 407 " --> pdb=" O   MET B 403 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ASP B 409 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 429
    Processing helix  chain 'C' and resid 17 through 35
    Processing helix  chain 'C' and resid 37 through 45
    Processing helix  chain 'C' and resid 45 through 59
      removed outlier: 3.659A  pdb=" N   GLY C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 74
      removed outlier: 3.526A  pdb=" N   SER C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL C  69 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 110
    Processing helix  chain 'C' and resid 131 through 138
    Processing helix  chain 'C' and resid 143 through 151
    Processing helix  chain 'C' and resid 152 through 171
      removed outlier: 3.721A  pdb=" N   VAL C 156 " --> pdb=" O   GLU C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 222
      removed outlier: 3.515A  pdb=" N   ARG C 179 " --> pdb=" O   GLU C 175 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR C 206 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG C 208 " --> pdb=" O   MET C 204 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   ILE C 209 " --> pdb=" O   GLN C 205 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE C 212 " --> pdb=" O   ARG C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 248
      removed outlier: 3.631A  pdb=" N   LYS C 232 " --> pdb=" O   GLY C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 256
      removed outlier: 3.538A  pdb=" N   LYS C 254 " --> pdb=" O   PHE C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 267
    Processing helix  chain 'C' and resid 267 through 278
      removed outlier: 3.720A  pdb=" N   MET C 271 " --> pdb=" O   ALA C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 294
      removed outlier: 3.751A  pdb=" N   THR C 287 " --> pdb=" O   THR C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 313
      removed outlier: 3.655A  pdb=" N   SER C 303 " --> pdb=" O   LYS C 299 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   PHE C 304 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      Proline residue:  C 307  - end of helix
    Processing helix  chain 'C' and resid 314 through 332
      removed outlier: 3.549A  pdb=" N   LEU C 326 " --> pdb=" O   GLY C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 355
      removed outlier: 3.655A  pdb=" N   VAL C 345 " --> pdb=" O   GLN C 341 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE C 353 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLY C 354 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 373
      removed outlier: 4.071A  pdb=" N   ILE C 364 " --> pdb=" O   GLY C 360 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET C 365 " --> pdb=" O   ALA C 361 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA C 367 " --> pdb=" O   ALA C 363 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   MET C 368 " --> pdb=" O   ILE C 364 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL C 369 " --> pdb=" O   MET C 365 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL C 373 " --> pdb=" O   VAL C 369 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 393
      removed outlier: 3.961A  pdb=" N   ALA C 388 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE C 393 " --> pdb=" O   MET C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 393 through 420
      removed outlier: 4.215A  pdb=" N   GLY C 400 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL C 404 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR C 407 " --> pdb=" O   MET C 403 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASP C 409 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 429

    701 hydrogen bonds defined for protein.
    2076 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: 1.38

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1406
        1.31 -     1.43: 2211
        1.43 -     1.56: 5454
        1.56 -     1.68: 0
        1.68 -     1.81: 96
  Bond restraints: 9167
  Sorted by residual:
  bond pdb=" C   PRO B  47 "
       pdb=" O   PRO B  47 "
    ideal  model  delta    sigma   weight residual
    1.237  1.186  0.051 1.32e-02 5.74e+03 1.51e+01
  bond pdb=" C   PRO A  47 "
       pdb=" O   PRO A  47 "
    ideal  model  delta    sigma   weight residual
    1.235  1.185  0.050 1.30e-02 5.92e+03 1.49e+01
  bond pdb=" C   PRO C  47 "
       pdb=" O   PRO C  47 "
    ideal  model  delta    sigma   weight residual
    1.235  1.188  0.048 1.30e-02 5.92e+03 1.34e+01
  bond pdb=" N   ILE C  45 "
       pdb=" CA  ILE C  45 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.21e-02 6.83e+03 1.04e+01
  bond pdb=" N   VAL C 383 "
       pdb=" CA  VAL C 383 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.41e-02 5.03e+03 5.87e+00
  ... (remaining 9162 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 12198
        1.42 -     2.84: 203
        2.84 -     4.26: 44
        4.26 -     5.68: 11
        5.68 -     7.10: 8
  Bond angle restraints: 12464
  Sorted by residual:
  angle pdb=" N   LEU C 385 "
        pdb=" CA  LEU C 385 "
        pdb=" C   LEU C 385 "
      ideal   model   delta    sigma   weight residual
     113.55  106.45    7.10 1.26e+00 6.30e-01 3.17e+01
  angle pdb=" N   PHE B  48 "
        pdb=" CA  PHE B  48 "
        pdb=" C   PHE B  48 "
      ideal   model   delta    sigma   weight residual
     112.90  106.74    6.16 1.31e+00 5.83e-01 2.21e+01
  angle pdb=" C   THR C 378 "
        pdb=" CA  THR C 378 "
        pdb=" CB  THR C 378 "
      ideal   model   delta    sigma   weight residual
     108.76  114.96   -6.20 1.37e+00 5.33e-01 2.05e+01
  angle pdb=" N   PHE A  48 "
        pdb=" CA  PHE A  48 "
        pdb=" C   PHE A  48 "
      ideal   model   delta    sigma   weight residual
     112.90  107.13    5.77 1.31e+00 5.83e-01 1.94e+01
  angle pdb=" N   PHE C  48 "
        pdb=" CA  PHE C  48 "
        pdb=" C   PHE C  48 "
      ideal   model   delta    sigma   weight residual
     112.90  107.13    5.77 1.31e+00 5.83e-01 1.94e+01
  ... (remaining 12459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.21: 4495
       13.21 -    26.42: 622
       26.42 -    39.64: 172
       39.64 -    52.85: 89
       52.85 -    66.06: 18
  Dihedral angle restraints: 5396
    sinusoidal: 1997
      harmonic: 3399
  Sorted by residual:
  dihedral pdb=" CG  ARG A 289 "
           pdb=" CD  ARG A 289 "
           pdb=" NE  ARG A 289 "
           pdb=" CZ  ARG A 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.67  -50.33     2      1.50e+01 4.44e-03 1.26e+01
  dihedral pdb=" CG  ARG B 289 "
           pdb=" CD  ARG B 289 "
           pdb=" NE  ARG B 289 "
           pdb=" CZ  ARG B 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.68  -50.32     2      1.50e+01 4.44e-03 1.26e+01
  dihedral pdb=" CG  ARG C 289 "
           pdb=" CD  ARG C 289 "
           pdb=" NE  ARG C 289 "
           pdb=" CZ  ARG C 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.70  -50.30     2      1.50e+01 4.44e-03 1.26e+01
  ... (remaining 5393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1181
       0.041 -    0.082: 318
       0.082 -    0.122: 57
       0.122 -    0.163: 3
       0.163 -    0.204: 2
  Chirality restraints: 1561
  Sorted by residual:
  chirality pdb=" CA  VAL C 383 "
            pdb=" N   VAL C 383 "
            pdb=" C   VAL C 383 "
            pdb=" CB  VAL C 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  VAL C 383 "
            pdb=" CA  VAL C 383 "
            pdb=" CG1 VAL C 383 "
            pdb=" CG2 VAL C 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.47e-01
  chirality pdb=" CA  PHE A  48 "
            pdb=" N   PHE A  48 "
            pdb=" C   PHE A  48 "
            pdb=" CB  PHE A  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1558 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C  44 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.38e+00
        pdb=" C   TYR C  44 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   TYR C  44 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ILE C  45 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 284 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO C 285 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C 285 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 285 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 284 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO B 285 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 285 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 285 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1571
        2.76 -     3.29: 9063
        3.29 -     3.83: 15332
        3.83 -     4.36: 18221
        4.36 -     4.90: 31938
  Nonbonded interactions: 76125
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 280 "
            pdb=" OXT ASP C 501 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER B 280 "
            pdb=" OXT ASP B 501 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER A 280 "
            pdb=" OXT ASP A 501 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   THR B 283 "
            pdb=" OG1 THR B 287 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   THR C 283 "
            pdb=" OG1 THR C 287 "
     model   vdw
     2.230 3.040
  ... (remaining 76120 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 16 through 114 or resid 129 through 501))
  selection = (chain 'C' and (resid 16 through 114 or resid 129 through 501))
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.840
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
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      :  0.003   0.051   9167  Z= 0.161
  Angle     :  0.484   7.098  12464  Z= 0.286
  Chirality :  0.036   0.204   1561
  Planarity :  0.004   0.047   1523
  Dihedral  : 14.988  66.061   3232
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 16.16 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.23), residues: 1193
  helix:  0.31 (0.16), residues: 996
  sheet:  None (None), residues: 0
  loop :  0.20 (0.45), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 289 
 TYR   0.006   0.001   TYR C 320 
 PHE   0.006   0.001   PHE B 302 
 TRP   0.003   0.000   TRP A  16 
 HIS   0.001   0.000   HIS C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9167)
  covalent geometry    : angle       0.48430 (12464)
  hydrogen bonds       : bond        0.24639 (  701)
  hydrogen bonds       : angle       6.99183 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.206 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 0.0835
  time to fit residues: 12.6010
Evaluate side-chains
  99 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  379 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.182149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.140300 restraints weight = 9047.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.93
r_work: 0.3200 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9167  Z= 0.137
  Angle     :  0.502   5.776  12464  Z= 0.260
  Chirality :  0.039   0.120   1561
  Planarity :  0.004   0.048   1523
  Dihedral  :  3.760  57.951   1284
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.68 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.25), residues: 1193
  helix:  1.47 (0.16), residues: 1002
  sheet:  None (None), residues: 0
  loop :  0.65 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  82 
 TYR   0.009   0.001   TYR B 387 
 PHE   0.016   0.001   PHE C 302 
 TRP   0.006   0.001   TRP A  16 
 HIS   0.001   0.000   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9167)
  covalent geometry    : angle       0.50220 (12464)
  hydrogen bonds       : bond        0.04946 (  701)
  hydrogen bonds       : angle       4.48788 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6949 (tpp) cc_final: 0.6699 (tpp)
REVERT: B   97 MET cc_start: 0.6853 (tpp) cc_final: 0.6652 (tpp)
REVERT: C   97 MET cc_start: 0.6948 (tpp) cc_final: 0.6709 (tpp)
  outliers start: 13
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0600
  time to fit residues: 9.8426
Evaluate side-chains
  98 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  101 PHE
Chi-restraints excluded: chain B residue  292 GLU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0980
   chunk 61 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 111 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.182059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.132799 restraints weight = 9076.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.87
r_work: 0.3241 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9167  Z= 0.118
  Angle     :  0.466   5.699  12464  Z= 0.241
  Chirality :  0.038   0.115   1561
  Planarity :  0.004   0.045   1523
  Dihedral  :  3.713  58.863   1281
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.99 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.25), residues: 1193
  helix:  1.80 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop :  0.60 (0.50), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 289 
 TYR   0.010   0.001   TYR B 387 
 PHE   0.013   0.001   PHE A 242 
 TRP   0.005   0.001   TRP A  16 
 HIS   0.001   0.000   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9167)
  covalent geometry    : angle       0.46606 (12464)
  hydrogen bonds       : bond        0.03954 (  701)
  hydrogen bonds       : angle       3.98330 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7287 (tpp) cc_final: 0.6938 (tpp)
REVERT: B   97 MET cc_start: 0.7274 (tpp) cc_final: 0.6957 (tpp)
REVERT: C   97 MET cc_start: 0.7388 (tpp) cc_final: 0.7065 (tpp)
  outliers start: 22
  outliers final: 11
  residues processed: 123
  average time/residue: 0.0574
  time to fit residues: 11.2759
Evaluate side-chains
  108 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 65 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0470
   chunk 85 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.3478

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.184041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.141452 restraints weight = 9171.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.77
r_work: 0.3292 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9167  Z= 0.107
  Angle     :  0.457   5.669  12464  Z= 0.234
  Chirality :  0.037   0.115   1561
  Planarity :  0.004   0.040   1523
  Dihedral  :  3.721  58.659   1281
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.05 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.25), residues: 1193
  helix:  1.91 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop :  0.60 (0.50), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  82 
 TYR   0.006   0.001   TYR B 387 
 PHE   0.013   0.001   PHE A 242 
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9167)
  covalent geometry    : angle       0.45686 (12464)
  hydrogen bonds       : bond        0.03516 (  701)
  hydrogen bonds       : angle       3.84221 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B  302 PHE cc_start: 0.7604 (p90) cc_final: 0.7362 (p90)
REVERT: C   97 MET cc_start: 0.7452 (tpp) cc_final: 0.7071 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0601
  time to fit residues: 10.3699
Evaluate side-chains
  103 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 30 optimal weight:    0.1980
   chunk 76 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0070
   chunk 39 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0050
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.3812

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.184616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141636 restraints weight = 9098.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.75
r_work: 0.3252 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9167  Z= 0.105
  Angle     :  0.444   5.612  12464  Z= 0.227
  Chirality :  0.037   0.127   1561
  Planarity :  0.003   0.036   1523
  Dihedral  :  3.665  58.429   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.05 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.25), residues: 1193
  helix:  1.99 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop :  0.60 (0.50), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 289 
 TYR   0.006   0.001   TYR C 320 
 PHE   0.011   0.001   PHE B 302 
 TRP   0.005   0.001   TRP A  16 
 HIS   0.000   0.000   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9167)
  covalent geometry    : angle       0.44420 (12464)
  hydrogen bonds       : bond        0.03399 (  701)
  hydrogen bonds       : angle       3.74797 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  242 PHE cc_start: 0.6630 (t80) cc_final: 0.6359 (t80)
REVERT: B   97 MET cc_start: 0.6980 (tpp) cc_final: 0.6641 (tpp)
  outliers start: 19
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0600
  time to fit residues: 10.7656
Evaluate side-chains
  106 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0670
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.1922

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.179158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.125038 restraints weight = 9170.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.71
r_work: 0.3198 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9167  Z= 0.150
  Angle     :  0.486   5.603  12464  Z= 0.250
  Chirality :  0.039   0.117   1561
  Planarity :  0.004   0.034   1523
  Dihedral  :  3.795  59.082   1281
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.63 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.25), residues: 1193
  helix:  1.93 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop :  0.48 (0.48), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 401 
 TYR   0.007   0.001   TYR C 238 
 PHE   0.019   0.001   PHE A 302 
 TRP   0.005   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9167)
  covalent geometry    : angle       0.48552 (12464)
  hydrogen bonds       : bond        0.04078 (  701)
  hydrogen bonds       : angle       3.97011 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7235 (tpp) cc_final: 0.6923 (tpp)
REVERT: A  242 PHE cc_start: 0.7075 (t80) cc_final: 0.6770 (t80)
REVERT: B   97 MET cc_start: 0.7222 (tpp) cc_final: 0.6927 (tpp)
REVERT: C   68 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8031 (mm)
REVERT: C   97 MET cc_start: 0.7203 (tpp) cc_final: 0.6944 (tpp)
REVERT: C  292 GLU cc_start: 0.7532 (tt0) cc_final: 0.7291 (tt0)
  outliers start: 25
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0671
  time to fit residues: 12.1534
Evaluate side-chains
  109 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9990
   chunk 110 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 81 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   chunk 99 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.180203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.126374 restraints weight = 9130.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.71
r_work: 0.3189 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9167  Z= 0.130
  Angle     :  0.467   5.619  12464  Z= 0.240
  Chirality :  0.038   0.117   1561
  Planarity :  0.004   0.035   1523
  Dihedral  :  3.784  59.794   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.73 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.25), residues: 1193
  helix:  1.94 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop :  0.44 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 401 
 TYR   0.006   0.001   TYR A 238 
 PHE   0.016   0.001   PHE A 302 
 TRP   0.005   0.001   TRP A  16 
 HIS   0.000   0.000   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9167)
  covalent geometry    : angle       0.46735 (12464)
  hydrogen bonds       : bond        0.03816 (  701)
  hydrogen bonds       : angle       3.91257 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7273 (tpp) cc_final: 0.6940 (tpp)
REVERT: A  242 PHE cc_start: 0.7031 (t80) cc_final: 0.6758 (t80)
REVERT: C   68 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7968 (mm)
REVERT: C   97 MET cc_start: 0.7235 (tpp) cc_final: 0.6945 (tpp)
REVERT: C  292 GLU cc_start: 0.7585 (tt0) cc_final: 0.7355 (tt0)
  outliers start: 24
  outliers final: 20
  residues processed: 116
  average time/residue: 0.0599
  time to fit residues: 10.9465
Evaluate side-chains
  116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 96 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0370
   chunk 70 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.180935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138012 restraints weight = 9137.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.78
r_work: 0.3247 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9167  Z= 0.120
  Angle     :  0.461   5.601  12464  Z= 0.236
  Chirality :  0.038   0.116   1561
  Planarity :  0.004   0.035   1523
  Dihedral  :  3.763  59.857   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.42 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.25), residues: 1193
  helix:  1.98 (0.17), residues: 1008
  sheet:  None (None), residues: 0
  loop :  0.48 (0.48), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 401 
 TYR   0.006   0.001   TYR A 238 
 PHE   0.015   0.001   PHE A 302 
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9167)
  covalent geometry    : angle       0.46057 (12464)
  hydrogen bonds       : bond        0.03659 (  701)
  hydrogen bonds       : angle       3.84547 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7204 (tpp) cc_final: 0.6841 (tpp)
REVERT: B   97 MET cc_start: 0.7180 (tpp) cc_final: 0.6898 (tpp)
REVERT: C   68 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7934 (mm)
REVERT: C   97 MET cc_start: 0.7185 (tpp) cc_final: 0.6861 (tpp)
  outliers start: 21
  outliers final: 20
  residues processed: 115
  average time/residue: 0.0692
  time to fit residues: 12.5342
Evaluate side-chains
  116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0980
   chunk 63 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.180860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.137912 restraints weight = 9165.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.78
r_work: 0.3246 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9167  Z= 0.121
  Angle     :  0.461   5.607  12464  Z= 0.237
  Chirality :  0.038   0.114   1561
  Planarity :  0.003   0.035   1523
  Dihedral  :  3.754  59.304   1281
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.42 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.25), residues: 1193
  helix:  2.00 (0.17), residues: 1009
  sheet:  None (None), residues: 0
  loop :  0.50 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  54 
 TYR   0.006   0.001   TYR A 238 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9167)
  covalent geometry    : angle       0.46053 (12464)
  hydrogen bonds       : bond        0.03643 (  701)
  hydrogen bonds       : angle       3.83828 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7220 (tpp) cc_final: 0.6856 (tpp)
REVERT: A  242 PHE cc_start: 0.6891 (t80) cc_final: 0.6622 (t80)
REVERT: C   68 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7940 (mm)
REVERT: C   97 MET cc_start: 0.7173 (tpp) cc_final: 0.6838 (tpp)
  outliers start: 24
  outliers final: 21
  residues processed: 118
  average time/residue: 0.0545
  time to fit residues: 10.3294
Evaluate side-chains
  119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   chunk 116 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 114 optimal weight:    0.1980
   chunk 100 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.6582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.181231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.138567 restraints weight = 9160.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.78
r_work: 0.3222 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9167  Z= 0.119
  Angle     :  0.466   7.471  12464  Z= 0.237
  Chirality :  0.038   0.116   1561
  Planarity :  0.003   0.035   1523
  Dihedral  :  3.732  58.910   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.73 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.25), residues: 1193
  helix:  2.00 (0.17), residues: 1016
  sheet:  None (None), residues: 0
  loop :  0.63 (0.49), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C  54 
 TYR   0.005   0.001   TYR A 238 
 PHE   0.014   0.001   PHE C 302 
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9167)
  covalent geometry    : angle       0.46578 (12464)
  hydrogen bonds       : bond        0.03602 (  701)
  hydrogen bonds       : angle       3.82488 ( 2076)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7028 (tpp) cc_final: 0.6634 (tpp)
REVERT: A  242 PHE cc_start: 0.6680 (t80) cc_final: 0.6446 (t80)
REVERT: B   97 MET cc_start: 0.6991 (tpp) cc_final: 0.6731 (tpp)
REVERT: C   68 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7858 (mm)
REVERT: C   97 MET cc_start: 0.7044 (tpp) cc_final: 0.6708 (tpp)
  outliers start: 22
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0707
  time to fit residues: 12.5878
Evaluate side-chains
  115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  320 TYR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  315 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  396 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 117 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 114 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.180658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138088 restraints weight = 9070.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.77
r_work: 0.3212 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9167  Z= 0.126
  Angle     :  0.475   7.124  12464  Z= 0.241
  Chirality :  0.038   0.115   1561
  Planarity :  0.003   0.035   1523
  Dihedral  :  3.751  58.803   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.63 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.25), residues: 1193
  helix:  2.02 (0.17), residues: 1009
  sheet:  None (None), residues: 0
  loop :  0.52 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 401 
 TYR   0.006   0.001   TYR A 238 
 PHE   0.015   0.001   PHE C 302 
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9167)
  covalent geometry    : angle       0.47479 (12464)
  hydrogen bonds       : bond        0.03703 (  701)
  hydrogen bonds       : angle       3.84942 ( 2076)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2150.57 seconds
wall clock time: 37 minutes 25.61 seconds (2245.61 seconds total)