Starting phenix.real_space_refine
on Sat Dec 28 17:11:50 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.012 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.93, per 1000 atoms: 0.66
  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: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.07
  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: 2.82

  Time building geometry restraints manager: 2.85 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 430 or resid 501))
  selection = (chain 'C' and (resid 16 through 114 or resid 129 through 430 or resid 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:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.340
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.840
-------------------------------------------------------------------------------
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= 0.170
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (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
 TRP   0.003   0.000   TRP A  16 
 HIS   0.001   0.000   HIS C 334 
 PHE   0.006   0.001   PHE B 302 
 TYR   0.006   0.001   TYR C 320 
 ARG   0.011   0.000   ARG B 289 

*********************** 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  : 0.903 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 0.2300
  time to fit residues: 34.4439
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  : 0.981 
-------------------------------------------------------------------------------
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 101 optimal weight:    6.9990
   chunk 90 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 94 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1701

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= 0.177
  Angle     :  0.497   5.762  12464  Z= 0.258
  Chirality :  0.039   0.122   1561
  Planarity :  0.004   0.048   1523
  Dihedral  :  3.775  58.435   1284
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.36 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.25), residues: 1193
  helix:  1.52 (0.16), residues: 1001
  sheet:  None (None), residues: 0
  loop :  0.69 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.001   0.000   HIS A  34 
 PHE   0.014   0.001   PHE A 302 
 TYR   0.009   0.001   TYR B 387 
 ARG   0.002   0.000   ARG C  82 

*********************** 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: 12
    poor density    : 98
  time to evaluate  : 1.022 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1643
  time to fit residues: 26.7268
Evaluate side-chains
  96 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain A residue  373 VAL
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 C residue  292 GLU
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 60 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0270
   chunk 30 optimal weight:    0.0570
   chunk 109 optimal weight:    5.9990
   chunk 117 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.5356

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9167  Z= 0.160
  Angle     :  0.462   5.647  12464  Z= 0.239
  Chirality :  0.038   0.118   1561
  Planarity :  0.004   0.045   1523
  Dihedral  :  3.693  58.462   1281
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.68 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.25), residues: 1193
  helix:  1.79 (0.17), residues: 1004
  sheet:  None (None), residues: 0
  loop :  0.60 (0.49), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  16 
 HIS   0.001   0.000   HIS C 334 
 PHE   0.013   0.001   PHE A 242 
 TYR   0.008   0.001   TYR B 387 
 ARG   0.001   0.000   ARG C 177 

*********************** 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
  124 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.023 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7503 (tpp) cc_final: 0.7290 (tpp)
  outliers start: 23
  outliers final: 10
  residues processed: 118
  average time/residue: 0.1605
  time to fit residues: 29.2819
Evaluate side-chains
  104 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  286 VAL
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 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 107 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0670
   chunk 57 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    0.6918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2207

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= 0.178
  Angle     :  0.471   5.660  12464  Z= 0.242
  Chirality :  0.038   0.128   1561
  Planarity :  0.004   0.042   1523
  Dihedral  :  3.738  59.123   1281
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.31 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.25), residues: 1193
  helix:  1.90 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop :  0.51 (0.49), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  16 
 HIS   0.001   0.000   HIS A  34 
 PHE   0.014   0.001   PHE A 242 
 TYR   0.006   0.001   TYR B 387 
 ARG   0.001   0.000   ARG B 289 

*********************** 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
  117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7518 (tpp) cc_final: 0.7258 (tpp)
  outliers start: 20
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1659
  time to fit residues: 29.2521
Evaluate side-chains
  111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
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  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  345 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0970
   chunk 1 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.6378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2317

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= 0.170
  Angle     :  0.459   5.718  12464  Z= 0.235
  Chirality :  0.038   0.116   1561
  Planarity :  0.004   0.037   1523
  Dihedral  :  3.728  58.715   1281
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.25), residues: 1193
  helix:  1.94 (0.17), residues: 1011
  sheet:  None (None), residues: 0
  loop :  0.57 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  16 
 HIS   0.000   0.000   HIS B 334 
 PHE   0.013   0.001   PHE C 302 
 TYR   0.006   0.001   TYR C 320 
 ARG   0.001   0.000   ARG B 289 

*********************** 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
  120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7558 (tpp) cc_final: 0.7285 (tpp)
REVERT: A  242 PHE cc_start: 0.7286 (t80) cc_final: 0.7022 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 117
  average time/residue: 0.1579
  time to fit residues: 28.6871
Evaluate side-chains
  111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
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  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  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 39 optimal weight:    0.9980
   chunk 104 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 116 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2421

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= 0.166
  Angle     :  0.453   5.605  12464  Z= 0.232
  Chirality :  0.038   0.115   1561
  Planarity :  0.004   0.035   1523
  Dihedral  :  3.727  58.900   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.25), residues: 1193
  helix:  1.99 (0.17), residues: 1011
  sheet:  None (None), residues: 0
  loop :  0.53 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 
 PHE   0.013   0.001   PHE A 302 
 TYR   0.006   0.001   TYR A 320 
 ARG   0.001   0.000   ARG C  54 

*********************** 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
  124 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7567 (tpp) cc_final: 0.7272 (tpp)
REVERT: A  242 PHE cc_start: 0.7291 (t80) cc_final: 0.7029 (t80)
REVERT: C   68 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8138 (mm)
  outliers start: 25
  outliers final: 17
  residues processed: 121
  average time/residue: 0.1645
  time to fit residues: 30.8255
Evaluate side-chains
  111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 65 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 64 optimal weight:    0.3980
   chunk 115 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2470

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= 0.160
  Angle     :  0.453   5.600  12464  Z= 0.232
  Chirality :  0.037   0.116   1561
  Planarity :  0.004   0.035   1523
  Dihedral  :  3.704  58.941   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.73 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.25), residues: 1193
  helix:  2.00 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop :  0.54 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS B 334 
 PHE   0.012   0.001   PHE C 302 
 TYR   0.007   0.001   TYR B 387 
 ARG   0.001   0.000   ARG B 401 

*********************** 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
  116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7560 (tpp) cc_final: 0.7268 (tpp)
REVERT: A  242 PHE cc_start: 0.7276 (t80) cc_final: 0.7055 (t80)
REVERT: C   68 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8123 (mm)
  outliers start: 23
  outliers final: 18
  residues processed: 114
  average time/residue: 0.1645
  time to fit residues: 29.2913
Evaluate side-chains
  111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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  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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0670
   chunk 22 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.9322

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9167  Z= 0.205
  Angle     :  0.474   5.613  12464  Z= 0.243
  Chirality :  0.038   0.116   1561
  Planarity :  0.003   0.035   1523
  Dihedral  :  3.771  59.678   1281
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.25), residues: 1193
  helix:  1.95 (0.17), residues: 1010
  sheet:  None (None), residues: 0
  loop :  0.51 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 
 PHE   0.016   0.001   PHE C 302 
 TYR   0.006   0.001   TYR A 238 
 ARG   0.001   0.000   ARG B 401 

*********************** 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
  117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7607 (tpp) cc_final: 0.7331 (tpp)
REVERT: A  242 PHE cc_start: 0.7327 (t80) cc_final: 0.7027 (t80)
REVERT: C   68 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8209 (mm)
  outliers start: 22
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1600
  time to fit residues: 27.6918
Evaluate side-chains
  115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
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  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   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  308 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 101 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0870
   chunk 33 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 113 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2506

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= 0.179
  Angle     :  0.465   5.595  12464  Z= 0.238
  Chirality :  0.038   0.118   1561
  Planarity :  0.003   0.036   1523
  Dihedral  :  3.749  59.660   1281
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.25), residues: 1193
  helix:  1.96 (0.17), residues: 1013
  sheet:  None (None), residues: 0
  loop :  0.60 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS C  34 
 PHE   0.013   0.001   PHE C 302 
 TYR   0.006   0.001   TYR B 387 
 ARG   0.001   0.000   ARG C  54 

*********************** 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
  114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7591 (tpp) cc_final: 0.7316 (tpp)
REVERT: A  242 PHE cc_start: 0.7294 (t80) cc_final: 0.7067 (t80)
REVERT: C   68 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8161 (mm)
  outliers start: 20
  outliers final: 19
  residues processed: 109
  average time/residue: 0.1680
  time to fit residues: 28.3080
Evaluate side-chains
  113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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  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   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  308 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 110 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9167  Z= 0.200
  Angle     :  0.478   6.771  12464  Z= 0.245
  Chirality :  0.038   0.115   1561
  Planarity :  0.003   0.036   1523
  Dihedral  :  3.767  58.842   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.25), residues: 1193
  helix:  1.96 (0.17), residues: 1012
  sheet:  None (None), residues: 0
  loop :  0.62 (0.48), residues: 181

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

********************** 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
  115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7581 (tpp) cc_final: 0.7315 (tpp)
REVERT: A  242 PHE cc_start: 0.7311 (t80) cc_final: 0.6998 (t80)
REVERT: C   68 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8193 (mm)
  outliers start: 20
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1811
  time to fit residues: 30.7342
Evaluate side-chains
  113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
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  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   68 LEU
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain C residue  308 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 95 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.181598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138354 restraints weight = 9067.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.87
r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2583

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= 0.171
  Angle     :  0.462   5.926  12464  Z= 0.237
  Chirality :  0.038   0.114   1561
  Planarity :  0.003   0.036   1523
  Dihedral  :  3.731  58.710   1281
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.25), residues: 1193
  helix:  2.01 (0.17), residues: 1016
  sheet:  None (None), residues: 0
  loop :  0.64 (0.49), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS B 334 
 PHE   0.012   0.001   PHE C 302 
 TYR   0.006   0.001   TYR B 387 
 ARG   0.001   0.000   ARG C  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1884.12 seconds
wall clock time: 35 minutes 17.15 seconds (2117.15 seconds total)