Starting phenix.real_space_refine
on Thu Feb 13 08:48:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afa_15393/02_2025/8afa_15393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afa_15393/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afa_15393/02_2025/8afa_15393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afa_15393/02_2025/8afa_15393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afa_15393/02_2025/8afa_15393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afa_15393/02_2025/8afa_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.47, per 1000 atoms: 0.61
  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: 2.17
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.79
  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: 2.68

  Time building geometry restraints manager: 2.52 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.560
  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:          0.370
  Check model and map are aligned:         0.090
  Set scattering table:                    0.080
  Process input model:                     22.150
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.340
-------------------------------------------------------------------------------
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  : 0.860 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 0.2127
  time to fit residues: 32.0048
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  : 0.960 
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.182929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.141277 restraints weight = 9042.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.02
r_work: 0.3223 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
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  : 0.861 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6894 (tpp) cc_final: 0.6632 (tpp)
REVERT: B   97 MET cc_start: 0.6806 (tpp) cc_final: 0.6593 (tpp)
REVERT: C   97 MET cc_start: 0.6882 (tpp) cc_final: 0.6633 (tpp)
  outliers start: 12
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1559
  time to fit residues: 25.4781
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  : 0.884 
-------------------------------------------------------------------------------
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 21 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 104 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.178725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.124454 restraints weight = 9155.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.73
r_work: 0.3155 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9167  Z= 0.232
  Angle     :  0.501   5.710  12464  Z= 0.259
  Chirality :  0.039   0.118   1561
  Planarity :  0.004   0.045   1523
  Dihedral  :  3.813  59.162   1281
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  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 (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:  2.16 (0.25), residues: 1193
  helix:  1.63 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop :  0.65 (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 C  34 
 PHE   0.018   0.001   PHE A 302 
 TYR   0.007   0.001   TYR A 238 
 ARG   0.001   0.000   ARG B 401 

*********************** 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
  121 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9016 (ttp) cc_final: 0.8796 (ttp)
REVERT: A   97 MET cc_start: 0.7196 (tpp) cc_final: 0.6903 (tpp)
REVERT: B   97 MET cc_start: 0.7169 (tpp) cc_final: 0.6907 (tpp)
REVERT: C   97 MET cc_start: 0.7161 (tpp) cc_final: 0.6895 (tpp)
  outliers start: 22
  outliers final: 13
  residues processed: 115
  average time/residue: 0.1630
  time to fit residues: 28.8576
Evaluate side-chains
  104 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 GLU
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  292 GLU
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  292 GLU
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 44 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.172935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130394 restraints weight = 9231.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.04
r_work: 0.3107 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   9167  Z= 0.449
  Angle     :  0.605   5.578  12464  Z= 0.316
  Chirality :  0.044   0.129   1561
  Planarity :  0.004   0.043   1523
  Dihedral  :  4.144  58.382   1281
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.58 %
    Favored  : 80.89 %
  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:  1.65 (0.24), residues: 1193
  helix:  1.25 (0.16), residues: 1003
  sheet:  None (None), residues: 0
  loop :  0.73 (0.48), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.001   0.000   HIS C  34 
 PHE   0.023   0.002   PHE C 302 
 TYR   0.009   0.002   TYR A  90 
 ARG   0.004   0.000   ARG B 401 

*********************** 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
  121 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6876 (tpp) cc_final: 0.6610 (tpp)
REVERT: B   97 MET cc_start: 0.6825 (tpp) cc_final: 0.6591 (tpp)
REVERT: C   97 MET cc_start: 0.7034 (tpp) cc_final: 0.6653 (tpp)
  outliers start: 24
  outliers final: 19
  residues processed: 117
  average time/residue: 0.1599
  time to fit residues: 29.4361
Evaluate side-chains
  114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  292 GLU
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  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  286 VAL
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  344 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 62 optimal weight:    0.0980
   chunk 27 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0980
   chunk 103 optimal weight:    8.9990
   chunk 119 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.180169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.126816 restraints weight = 9172.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.73
r_work: 0.3228 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2386

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= 0.161
  Angle     :  0.470   5.676  12464  Z= 0.243
  Chirality :  0.038   0.118   1561
  Planarity :  0.004   0.043   1523
  Dihedral  :  3.880  58.450   1281
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.47 %
    Favored  : 81.20 %
  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:  2.31 (0.25), residues: 1193
  helix:  1.73 (0.17), residues: 1007
  sheet:  None (None), residues: 0
  loop :  0.72 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 428 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.020   0.001   PHE B 242 
 TYR   0.007   0.001   TYR C 217 
 ARG   0.001   0.000   ARG C 177 

*********************** 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: 22
    poor density    : 98
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7255 (tpp) cc_final: 0.6941 (tpp)
REVERT: A  219 MET cc_start: 0.8189 (mmp) cc_final: 0.7809 (mmp)
REVERT: B   97 MET cc_start: 0.7176 (tpp) cc_final: 0.6877 (tpp)
REVERT: C   68 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7896 (mm)
REVERT: C   97 MET cc_start: 0.7313 (tpp) cc_final: 0.7023 (tpp)
  outliers start: 22
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1507
  time to fit residues: 26.7986
Evaluate side-chains
  105 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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  373 VAL
Chi-restraints excluded: chain A residue  391 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    0.0000
   chunk 118 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 91 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0470
   chunk 81 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9686

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.178096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135675 restraints weight = 9115.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.96
r_work: 0.3180 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2442

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= 0.210
  Angle     :  0.482   5.697  12464  Z= 0.248
  Chirality :  0.038   0.117   1561
  Planarity :  0.004   0.040   1523
  Dihedral  :  3.854  59.250   1281
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.53 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.38 (0.25), residues: 1193
  helix:  1.78 (0.17), residues: 1007
  sheet:  None (None), residues: 0
  loop :  0.74 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.018   0.001   PHE B 242 
 TYR   0.007   0.001   TYR C 238 
 ARG   0.001   0.000   ARG A 401 

*********************** 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
  119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7304 (tpp) cc_final: 0.7000 (tpp)
REVERT: B   97 MET cc_start: 0.7283 (tpp) cc_final: 0.6998 (tpp)
REVERT: C   68 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7958 (mm)
REVERT: C   97 MET cc_start: 0.7354 (tpp) cc_final: 0.7078 (tpp)
  outliers start: 20
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1506
  time to fit residues: 27.2331
Evaluate side-chains
  110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  373 VAL
Chi-restraints excluded: chain A residue  391 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 80 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 99 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.174894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132174 restraints weight = 9275.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.07
r_work: 0.3106 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9167  Z= 0.325
  Angle     :  0.539   5.664  12464  Z= 0.278
  Chirality :  0.041   0.121   1561
  Planarity :  0.004   0.037   1523
  Dihedral  :  3.999  57.722   1281
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.32 %
    Favored  : 79.83 %
  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:  2.11 (0.25), residues: 1193
  helix:  1.59 (0.16), residues: 1004
  sheet:  None (None), residues: 0
  loop :  0.70 (0.48), 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  34 
 PHE   0.023   0.002   PHE A 302 
 TYR   0.008   0.001   TYR A 238 
 ARG   0.002   0.000   ARG A 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
  122 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7238 (tpp) cc_final: 0.6940 (tpp)
REVERT: B   97 MET cc_start: 0.7206 (tpp) cc_final: 0.6960 (tpp)
REVERT: C   68 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8010 (mm)
REVERT: C   97 MET cc_start: 0.7309 (tpp) cc_final: 0.7026 (tpp)
  outliers start: 27
  outliers final: 20
  residues processed: 116
  average time/residue: 0.1570
  time to fit residues: 28.1039
Evaluate side-chains
  114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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   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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 62 optimal weight:    0.0770
   chunk 108 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 106 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 112 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.9542

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.177892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.135543 restraints weight = 9217.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.98
r_work: 0.3151 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2518

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= 0.210
  Angle     :  0.501   7.668  12464  Z= 0.253
  Chirality :  0.039   0.132   1561
  Planarity :  0.004   0.038   1523
  Dihedral  :  3.894  57.104   1281
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.68 %
    Favored  : 80.89 %
  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:  2.30 (0.25), residues: 1193
  helix:  1.73 (0.17), residues: 1008
  sheet:  None (None), residues: 0
  loop :  0.66 (0.49), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.027   0.001   PHE A 242 
 TYR   0.007   0.001   TYR B 217 
 ARG   0.001   0.000   ARG A 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
  116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7283 (tpp) cc_final: 0.6999 (tpp)
REVERT: A  314 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6320 (mtm)
REVERT: B   61 MET cc_start: 0.8782 (mmt) cc_final: 0.8553 (mmt)
REVERT: B   97 MET cc_start: 0.7261 (tpp) cc_final: 0.6987 (tpp)
REVERT: C   68 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7909 (mm)
REVERT: C   97 MET cc_start: 0.7371 (tpp) cc_final: 0.7102 (tpp)
  outliers start: 23
  outliers final: 18
  residues processed: 112
  average time/residue: 0.1592
  time to fit residues: 27.6716
Evaluate side-chains
  109 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
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  314 MET
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   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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 118 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.177729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.127805 restraints weight = 9195.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.94
r_work: 0.3187 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9167  Z= 0.217
  Angle     :  0.501   6.654  12464  Z= 0.254
  Chirality :  0.039   0.132   1561
  Planarity :  0.004   0.037   1523
  Dihedral  :  3.859  56.661   1281
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.47 %
    Favored  : 81.31 %
  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:  2.35 (0.25), residues: 1193
  helix:  1.76 (0.17), residues: 1008
  sheet:  None (None), residues: 0
  loop :  0.71 (0.50), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.024   0.001   PHE A 242 
 TYR   0.007   0.001   TYR C 238 
 ARG   0.001   0.000   ARG A 401 

*********************** 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
  113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7258 (tpp) cc_final: 0.6954 (tpp)
REVERT: A  314 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6295 (mtm)
REVERT: B   97 MET cc_start: 0.7199 (tpp) cc_final: 0.6899 (tpp)
REVERT: C   68 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7998 (mm)
REVERT: C   97 MET cc_start: 0.7301 (tpp) cc_final: 0.7019 (tpp)
  outliers start: 21
  outliers final: 18
  residues processed: 109
  average time/residue: 0.1649
  time to fit residues: 29.0415
Evaluate side-chains
  112 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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  314 MET
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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.179095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.136822 restraints weight = 9195.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.95
r_work: 0.3191 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2576

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= 0.185
  Angle     :  0.484   6.802  12464  Z= 0.244
  Chirality :  0.038   0.115   1561
  Planarity :  0.004   0.037   1523
  Dihedral  :  3.803  56.205   1281
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.47 %
    Favored  : 81.41 %
  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:  1.87 (0.17), residues: 1008
  sheet:  None (None), residues: 0
  loop :  0.72 (0.50), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  20 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.017   0.001   PHE A 302 
 TYR   0.007   0.001   TYR C 387 
 ARG   0.001   0.000   ARG C  54 

********************** 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
  113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A   97 MET cc_start: 0.7015 (tpp) cc_final: 0.6657 (tpp)
REVERT: A  242 PHE cc_start: 0.6762 (t80) cc_final: 0.6549 (t80)
REVERT: A  314 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6114 (mtm)
REVERT: B   97 MET cc_start: 0.6983 (tpp) cc_final: 0.6639 (tpp)
REVERT: C   68 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7896 (mm)
REVERT: C   97 MET cc_start: 0.7097 (tpp) cc_final: 0.6769 (tpp)
  outliers start: 20
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1535
  time to fit residues: 26.0505
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  : 0.901 
-------------------------------------------------------------------------------
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  314 MET
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   68 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  286 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 89 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.178760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.136466 restraints weight = 9181.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.96
r_work: 0.3184 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2601

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= 0.192
  Angle     :  0.486   6.563  12464  Z= 0.245
  Chirality :  0.038   0.116   1561
  Planarity :  0.004   0.037   1523
  Dihedral  :  3.790  55.905   1281
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.37 %
    Favored  : 81.31 %
  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:  2.54 (0.25), residues: 1193
  helix:  1.90 (0.17), residues: 1008
  sheet:  None (None), residues: 0
  loop :  0.73 (0.50), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  16 
 HIS   0.000   0.000   HIS B  34 
 PHE   0.018   0.001   PHE A 302 
 TYR   0.006   0.001   TYR B 217 
 ARG   0.001   0.000   ARG A 401 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4478.17 seconds
wall clock time: 80 minutes 3.66 seconds (4803.66 seconds total)