Starting phenix.real_space_refine
on Tue Jun 10 09:16:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zxp_60548/06_2025/8zxp_60548.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zxp_60548/06_2025/8zxp_60548.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zxp_60548/06_2025/8zxp_60548.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zxp_60548/06_2025/8zxp_60548.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zxp_60548/06_2025/8zxp_60548.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zxp_60548/06_2025/8zxp_60548.cif"
  }
  resolution = 3.09
  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=   0.004 sd=   0.048
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    7806      2.51       5
     N    1779      2.21       5
     O    1953      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3858
          Classifications: {'peptide': 494}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 474}
    Chain: "B"
      Number of atoms: 3858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3858
          Classifications: {'peptide': 494}
          Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 473}
    Chain: "C"
      Number of atoms: 3858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3858
          Classifications: {'peptide': 494}
          Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 474}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'KEN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'KEN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'KEN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.38, per 1000 atoms: 0.64
  Number of scatterers: 11586
  At special positions: 0
  Unit cell: (116.6, 115.54, 78.44, 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    1953      8.00
     N    1779      7.00
     C    7806      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.95
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2694

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 0 sheets defined
      83.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 34
      removed outlier: 4.227A  pdb=" N   ILE A  19 " --> pdb=" O   PRO A  15 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 74
      removed outlier: 3.583A  pdb=" N   TRP A  42 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      Proline residue:  A  44  - end of helix
      removed outlier: 6.272A  pdb=" N   TRP A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   PHE A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 3.513A  pdb=" N   ARG A  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE A  80 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 103
      removed outlier: 3.830A  pdb=" N   ALA A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR A 103 " --> pdb=" O   MET A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 113
    Processing helix  chain 'A' and resid 114 through 123
    Processing helix  chain 'A' and resid 130 through 146
      removed outlier: 3.549A  pdb=" N   ALA A 134 " --> pdb=" O   THR A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 167
      removed outlier: 3.504A  pdb=" N   TRP A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 153 " --> pdb=" O   HIS A 149 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   TYR A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 179
      removed outlier: 3.961A  pdb=" N   PHE A 178 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR A 179 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 175 through 179'
    Processing helix  chain 'A' and resid 184 through 188
      removed outlier: 3.982A  pdb=" N   HIS A 187 " --> pdb=" O   GLU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 216
    Processing helix  chain 'A' and resid 217 through 226
    Processing helix  chain 'A' and resid 233 through 250
      removed outlier: 3.577A  pdb=" N   ILE A 237 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 238 " --> pdb=" O   GLN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 279
    Processing helix  chain 'A' and resid 280 through 298
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.528A  pdb=" N   THR A 304 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 329
    Processing helix  chain 'A' and resid 329 through 341
      removed outlier: 3.547A  pdb=" N   VAL A 333 " --> pdb=" O   TRP A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 379
      removed outlier: 4.925A  pdb=" N   VAL A 356 " --> pdb=" O   GLY A 352 " (cutoff:3.500A)
      Proline residue:  A 357  - end of helix
      removed outlier: 3.922A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 379 " --> pdb=" O   THR A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
    Processing helix  chain 'A' and resid 393 through 401
      removed outlier: 4.140A  pdb=" N   ASN A 401 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 435
      removed outlier: 3.584A  pdb=" N   SER A 423 " --> pdb=" O   PHE A 419 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ASP A 425 " --> pdb=" O   ILE A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 464
    Processing helix  chain 'A' and resid 466 through 479
      removed outlier: 3.973A  pdb=" N   LEU A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 501
      removed outlier: 3.588A  pdb=" N   ALA A 501 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 34
      removed outlier: 4.036A  pdb=" N   ILE B  19 " --> pdb=" O   PRO B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 74
      Proline residue:  B  44  - end of helix
      removed outlier: 6.138A  pdb=" N   TRP B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   PHE B  57 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 80
      removed outlier: 3.655A  pdb=" N   ILE B  80 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 104
      removed outlier: 3.608A  pdb=" N   THR B 103 " --> pdb=" O   MET B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 112
    Processing helix  chain 'B' and resid 114 through 123
    Processing helix  chain 'B' and resid 131 through 146
    Processing helix  chain 'B' and resid 147 through 167
      removed outlier: 3.575A  pdb=" N   TRP B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE B 153 " --> pdb=" O   HIS B 149 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   TYR B 154 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 184 through 187
      removed outlier: 3.889A  pdb=" N   HIS B 187 " --> pdb=" O   GLU B 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 184 through 187'
    Processing helix  chain 'B' and resid 191 through 226
    Processing helix  chain 'B' and resid 230 through 250
    Processing helix  chain 'B' and resid 258 through 279
    Processing helix  chain 'B' and resid 280 through 298
    Processing helix  chain 'B' and resid 298 through 304
    Processing helix  chain 'B' and resid 313 through 318
      removed outlier: 4.221A  pdb=" N   VAL B 317 " --> pdb=" O   GLY B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 329
    Processing helix  chain 'B' and resid 329 through 341
    Processing helix  chain 'B' and resid 345 through 379
      removed outlier: 4.947A  pdb=" N   VAL B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      Proline residue:  B 357  - end of helix
      removed outlier: 3.911A  pdb=" N   SER B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY B 379 " --> pdb=" O   THR B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 3.595A  pdb=" N   ALA B 385 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 401
      removed outlier: 3.703A  pdb=" N   ASN B 401 " --> pdb=" O   VAL B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 437
      removed outlier: 3.561A  pdb=" N   SER B 423 " --> pdb=" O   PHE B 419 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   SER B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU B 429 " --> pdb=" O   ASP B 425 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL B 430 " --> pdb=" O   SER B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 464
      removed outlier: 3.715A  pdb=" N   PHE B 449 " --> pdb=" O   TRP B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 479
      removed outlier: 4.054A  pdb=" N   LEU B 470 " --> pdb=" O   GLY B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 501
      removed outlier: 3.528A  pdb=" N   ALA B 501 " --> pdb=" O   LYS B 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 34
    Processing helix  chain 'C' and resid 38 through 74
      removed outlier: 3.681A  pdb=" N   TRP C  42 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      Proline residue:  C  44  - end of helix
      removed outlier: 6.196A  pdb=" N   TRP C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   PHE C  57 " --> pdb=" O   ASN C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 80
      removed outlier: 3.572A  pdb=" N   ARG C  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE C  80 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 104
      removed outlier: 3.676A  pdb=" N   ALA C  98 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR C 103 " --> pdb=" O   MET C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 112
      removed outlier: 3.548A  pdb=" N   PHE C 112 " --> pdb=" O   GLY C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 123
    Processing helix  chain 'C' and resid 130 through 146
    Processing helix  chain 'C' and resid 147 through 167
      removed outlier: 3.664A  pdb=" N   TRP C 151 " --> pdb=" O   GLY C 147 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ILE C 153 " --> pdb=" O   HIS C 149 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   TYR C 154 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 177
      No H-bonds generated for 'chain 'C' and resid 175 through 177'
    Processing helix  chain 'C' and resid 178 through 183
    Processing helix  chain 'C' and resid 184 through 187
      removed outlier: 3.923A  pdb=" N   HIS C 187 " --> pdb=" O   GLU C 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 184 through 187'
    Processing helix  chain 'C' and resid 191 through 226
    Processing helix  chain 'C' and resid 232 through 250
      removed outlier: 3.721A  pdb=" N   GLY C 236 " --> pdb=" O   MET C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 279
    Processing helix  chain 'C' and resid 280 through 298
    Processing helix  chain 'C' and resid 298 through 304
      removed outlier: 3.567A  pdb=" N   THR C 304 " --> pdb=" O   ILE C 300 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 329
    Processing helix  chain 'C' and resid 329 through 341
    Processing helix  chain 'C' and resid 345 through 379
      removed outlier: 4.950A  pdb=" N   VAL C 356 " --> pdb=" O   GLY C 352 " (cutoff:3.500A)
      Proline residue:  C 357  - end of helix
      removed outlier: 3.894A  pdb=" N   SER C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY C 379 " --> pdb=" O   THR C 375 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 390
    Processing helix  chain 'C' and resid 393 through 401
      removed outlier: 3.864A  pdb=" N   ASN C 401 " --> pdb=" O   VAL C 397 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 437
      removed outlier: 3.565A  pdb=" N   SER C 423 " --> pdb=" O   PHE C 419 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   SER C 424 " --> pdb=" O   PHE C 420 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASP C 425 " --> pdb=" O   ILE C 421 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU C 429 " --> pdb=" O   ASP C 425 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   VAL C 430 " --> pdb=" O   SER C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 464
    Processing helix  chain 'C' and resid 466 through 479
      removed outlier: 4.110A  pdb=" N   LEU C 470 " --> pdb=" O   GLY C 466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 503

    854 hydrogen bonds defined for protein.
    2547 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: 3.57

  Time building geometry restraints manager: 3.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3313
        1.34 -     1.46: 2892
        1.46 -     1.58: 5645
        1.58 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 11940
  Sorted by residual:
  bond pdb=" C   SER C 230 "
       pdb=" N   PRO C 231 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.37e+00
  bond pdb=" CA  VAL A 444 "
       pdb=" CB  VAL A 444 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.021 1.05e-02 9.07e+03 3.93e+00
  bond pdb=" CB  GLU C 184 "
       pdb=" CG  GLU C 184 "
    ideal  model  delta    sigma   weight residual
    1.520  1.575 -0.055 3.00e-02 1.11e+03 3.37e+00
  bond pdb=" CB  TRP C 323 "
       pdb=" CG  TRP C 323 "
    ideal  model  delta    sigma   weight residual
    1.498  1.554 -0.056 3.10e-02 1.04e+03 3.21e+00
  bond pdb=" CB  TRP A 323 "
       pdb=" CG  TRP A 323 "
    ideal  model  delta    sigma   weight residual
    1.498  1.550 -0.052 3.10e-02 1.04e+03 2.84e+00
  ... (remaining 11935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 15949
        2.82 -     5.64: 266
        5.64 -     8.46: 61
        8.46 -    11.28: 14
       11.28 -    14.09: 3
  Bond angle restraints: 16293
  Sorted by residual:
  angle pdb=" N   TRP B 445 "
        pdb=" CA  TRP B 445 "
        pdb=" C   TRP B 445 "
      ideal   model   delta    sigma   weight residual
     114.62  107.58    7.04 1.14e+00 7.69e-01 3.81e+01
  angle pdb=" C   GLY C 106 "
        pdb=" N   ILE C 107 "
        pdb=" CA  ILE C 107 "
      ideal   model   delta    sigma   weight residual
     121.70  132.21  -10.51 1.80e+00 3.09e-01 3.41e+01
  angle pdb=" C   GLU C 441 "
        pdb=" N   SER C 442 "
        pdb=" CA  SER C 442 "
      ideal   model   delta    sigma   weight residual
     121.70  131.96  -10.26 1.80e+00 3.09e-01 3.25e+01
  angle pdb=" C   GLY B 256 "
        pdb=" N   VAL B 257 "
        pdb=" CA  VAL B 257 "
      ideal   model   delta    sigma   weight residual
     121.70  131.74  -10.04 1.80e+00 3.09e-01 3.11e+01
  angle pdb=" CA  ILE B  19 "
        pdb=" CB  ILE B  19 "
        pdb=" CG1 ILE B  19 "
      ideal   model   delta    sigma   weight residual
     110.40  118.67   -8.27 1.70e+00 3.46e-01 2.37e+01
  ... (remaining 16288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 5579
       17.12 -    34.25: 815
       34.25 -    51.37: 215
       51.37 -    68.50: 34
       68.50 -    85.62: 5
  Dihedral angle restraints: 6648
    sinusoidal: 2442
      harmonic: 4206
  Sorted by residual:
  dihedral pdb=" CA  ASN C  14 "
           pdb=" C   ASN C  14 "
           pdb=" N   PRO C  15 "
           pdb=" CA  PRO C  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.07   28.93     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  ASN B  14 "
           pdb=" C   ASN B  14 "
           pdb=" N   PRO B  15 "
           pdb=" CA  PRO B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.17   27.83     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" CA  ASN A  14 "
           pdb=" C   ASN A  14 "
           pdb=" N   PRO A  15 "
           pdb=" CA  PRO A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.35   25.65     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 6645 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1531
       0.063 -    0.126: 287
       0.126 -    0.188: 56
       0.188 -    0.251: 6
       0.251 -    0.314: 1
  Chirality restraints: 1881
  Sorted by residual:
  chirality pdb=" CB  THR A 472 "
            pdb=" CA  THR A 472 "
            pdb=" OG1 THR A 472 "
            pdb=" CG2 THR A 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  ILE A 229 "
            pdb=" CA  ILE A 229 "
            pdb=" CG1 ILE A 229 "
            pdb=" CG2 ILE A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  ILE A 109 "
            pdb=" CA  ILE A 109 "
            pdb=" CG1 ILE A 109 "
            pdb=" CG2 ILE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1878 not shown)

  Planarity restraints: 1962
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 444 "   -0.017 2.00e-02 2.50e+03   3.40e-02 1.15e+01
        pdb=" C   VAL B 444 "    0.059 2.00e-02 2.50e+03
        pdb=" O   VAL B 444 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   TRP B 445 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 230 "    0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO A 231 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 231 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 231 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 444 "   -0.016 2.00e-02 2.50e+03   3.16e-02 9.98e+00
        pdb=" C   VAL A 444 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL A 444 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   TRP A 445 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1959 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3432
        2.82 -     3.34: 10813
        3.34 -     3.86: 20371
        3.86 -     4.38: 21995
        4.38 -     4.90: 40265
  Nonbonded interactions: 96876
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 248 "
            pdb=" O   LYS C 255 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   THR A 103 "
            pdb=" OG1 THR A 103 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ALA A  27 "
            pdb=" OG1 THR A  31 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ALA C  27 "
            pdb=" OG1 THR C  31 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   GLY C 313 "
            pdb=" ND2 ASN C 316 "
     model   vdw
     2.342 3.120
  ... (remaining 96871 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.460
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     29.110
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.060
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
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      :  0.005   0.067  11941  Z= 0.234
  Angle     :  0.984  14.094  16293  Z= 0.537
  Chirality :  0.052   0.314   1881
  Planarity :  0.007   0.104   1962
  Dihedral  : 16.926  85.619   3954
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 29.32 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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: -1.54 (0.18), residues: 1476
  helix: -0.64 (0.13), residues: 1092
  sheet:  None (None), residues: 0
  loop : -1.74 (0.27), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP C 329 
 HIS   0.008   0.002   HIS B 192 
 PHE   0.041   0.002   PHE C 420 
 TYR   0.013   0.001   TYR A 154 
 ARG   0.013   0.001   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11536 (  854)
  hydrogen bonds       : angle       6.47912 ( 2547)
  covalent geometry    : bond        0.00487 (11940)
  covalent geometry    : angle       0.98370 (16293)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 160
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  429 LEU cc_start: 0.7432 (tp) cc_final: 0.7111 (mp)
REVERT: A  481 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: B  332 PHE cc_start: 0.8263 (t80) cc_final: 0.7793 (t80)
REVERT: C  140 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7523 (pt0)
REVERT: C  168 ARG cc_start: 0.8533 (mmt-90) cc_final: 0.8114 (mpt180)
  outliers start: 5
  outliers final: 1
  residues processed: 164
  average time/residue: 0.2449
  time to fit residues: 57.3760
Evaluate side-chains
  154 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 151
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain C residue  140 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.152196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.111532 restraints weight = 15143.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.15
r_work: 0.3150 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11941  Z= 0.136
  Angle     :  0.561   7.752  16293  Z= 0.297
  Chirality :  0.039   0.167   1881
  Planarity :  0.004   0.073   1962
  Dihedral  :  4.960  57.266   1545
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.25 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 25.23 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  0.63 (0.21), residues: 1476
  helix:  1.05 (0.15), residues: 1095
  sheet:  None (None), residues: 0
  loop : -1.32 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 329 
 HIS   0.002   0.001   HIS A 149 
 PHE   0.028   0.001   PHE B 420 
 TYR   0.017   0.001   TYR C 154 
 ARG   0.005   0.001   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  854)
  hydrogen bonds       : angle       4.50668 ( 2547)
  covalent geometry    : bond        0.00309 (11940)
  covalent geometry    : angle       0.56111 (16293)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.6759 (ttm110) cc_final: 0.6536 (ttp-110)
REVERT: A  447 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7492 (mmm-85)
REVERT: A  481 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7627 (m-80)
REVERT: B  185 ARG cc_start: 0.7171 (ttp-110) cc_final: 0.6707 (mtp85)
REVERT: B  332 PHE cc_start: 0.8338 (t80) cc_final: 0.8126 (t80)
REVERT: B  344 ARG cc_start: 0.8459 (mmt180) cc_final: 0.8146 (mmt180)
REVERT: B  429 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7301 (tt)
REVERT: B  481 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7947 (m-80)
REVERT: B  488 MET cc_start: 0.8061 (tmm) cc_final: 0.7625 (ttp)
REVERT: C   38 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6609 (tppt)
REVERT: C  156 MET cc_start: 0.8047 (mmm) cc_final: 0.7685 (mmm)
REVERT: C  481 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7974 (m-80)
  outliers start: 38
  outliers final: 20
  residues processed: 193
  average time/residue: 0.2317
  time to fit residues: 63.9241
Evaluate side-chains
  179 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  419 PHE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  460 VAL
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  484 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 134 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 98 optimal weight:    8.9990
   chunk 136 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0060
   chunk 3 optimal weight:    0.9990
   chunk 139 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110157 restraints weight = 15112.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.16
r_work: 0.3143 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11941  Z= 0.129
  Angle     :  0.538   6.013  16293  Z= 0.282
  Chirality :  0.039   0.171   1881
  Planarity :  0.004   0.071   1962
  Dihedral  :  4.654  59.147   1541
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.18 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.96 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  1.43 (0.22), residues: 1476
  helix:  1.64 (0.16), residues: 1098
  sheet:  None (None), residues: 0
  loop : -1.09 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 329 
 HIS   0.002   0.001   HIS B 192 
 PHE   0.024   0.001   PHE B 420 
 TYR   0.008   0.001   TYR B 295 
 ARG   0.003   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  854)
  hydrogen bonds       : angle       4.20269 ( 2547)
  covalent geometry    : bond        0.00292 (11940)
  covalent geometry    : angle       0.53808 (16293)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 158
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.6838 (ttm110) cc_final: 0.6586 (ttp-110)
REVERT: A  262 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6384 (t0)
REVERT: A  447 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7573 (mmm160)
REVERT: A  481 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7481 (m-80)
REVERT: B  131 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7108 (t0)
REVERT: B  185 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.6655 (mtp85)
REVERT: B  481 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7868 (m-80)
REVERT: B  488 MET cc_start: 0.8070 (tmm) cc_final: 0.7824 (ttp)
REVERT: C   38 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6616 (tppt)
REVERT: C   91 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6572 (t80)
REVERT: C  481 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7868 (m-80)
REVERT: C  499 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7566 (tp30)
  outliers start: 53
  outliers final: 22
  residues processed: 190
  average time/residue: 0.2389
  time to fit residues: 64.9528
Evaluate side-chains
  178 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  262 ASN
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  131 ASP
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  417 PHE
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 83 optimal weight:    0.0770
   chunk 2 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 140 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
C 120 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.109760 restraints weight = 14909.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.06
r_work: 0.3121 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11941  Z= 0.140
  Angle     :  0.542   6.495  16293  Z= 0.283
  Chirality :  0.040   0.172   1881
  Planarity :  0.004   0.068   1962
  Dihedral  :  4.557  57.193   1541
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.05 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.70 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  1.67 (0.22), residues: 1476
  helix:  1.82 (0.16), residues: 1098
  sheet:  None (None), residues: 0
  loop : -1.02 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 329 
 HIS   0.002   0.001   HIS A 145 
 PHE   0.022   0.001   PHE B 420 
 TYR   0.009   0.001   TYR C 295 
 ARG   0.002   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  854)
  hydrogen bonds       : angle       4.14483 ( 2547)
  covalent geometry    : bond        0.00324 (11940)
  covalent geometry    : angle       0.54161 (16293)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 165
  time to evaluate  : 1.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.6722 (ttm110) cc_final: 0.6466 (ttp-110)
REVERT: A  447 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7394 (mmm160)
REVERT: A  481 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7535 (m-80)
REVERT: A  483 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7627 (p)
REVERT: B  185 ARG cc_start: 0.6973 (ttp-110) cc_final: 0.6486 (mtp85)
REVERT: B  429 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7455 (tt)
REVERT: B  481 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7956 (m-80)
REVERT: C   38 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6587 (tppt)
REVERT: C   91 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6583 (t80)
REVERT: C  481 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8142 (m-80)
REVERT: C  499 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7500 (tp30)
  outliers start: 50
  outliers final: 25
  residues processed: 196
  average time/residue: 0.2667
  time to fit residues: 74.8389
Evaluate side-chains
  187 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  419 PHE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  417 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 112 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.110176 restraints weight = 14876.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.07
r_work: 0.3122 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11941  Z= 0.128
  Angle     :  0.533   6.078  16293  Z= 0.279
  Chirality :  0.039   0.164   1881
  Planarity :  0.004   0.065   1962
  Dihedral  :  4.471  55.296   1541
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.46 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.27 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  1.84 (0.22), residues: 1476
  helix:  1.94 (0.16), residues: 1098
  sheet:  None (None), residues: 0
  loop : -0.95 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 329 
 HIS   0.002   0.001   HIS B 192 
 PHE   0.028   0.001   PHE A 332 
 TYR   0.026   0.001   TYR C 154 
 ARG   0.003   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  854)
  hydrogen bonds       : angle       4.08128 ( 2547)
  covalent geometry    : bond        0.00293 (11940)
  covalent geometry    : angle       0.53281 (16293)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 164
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TRP cc_start: 0.7366 (m-10) cc_final: 0.7156 (m-10)
REVERT: A  185 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6535 (ttp-110)
REVERT: A  233 MET cc_start: 0.7024 (tpp) cc_final: 0.6705 (tpp)
REVERT: A  447 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7356 (mmm160)
REVERT: A  481 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7592 (m-80)
REVERT: A  483 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7594 (p)
REVERT: B   99 MET cc_start: 0.8167 (ttt) cc_final: 0.7848 (ptm)
REVERT: B  185 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6491 (mtp85)
REVERT: B  429 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7465 (tt)
REVERT: B  481 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7827 (m-80)
REVERT: C   38 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6546 (tppt)
REVERT: C   91 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6409 (t80)
REVERT: C  228 GLU cc_start: 0.7005 (pt0) cc_final: 0.6588 (pm20)
REVERT: C  481 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8135 (m-80)
REVERT: C  499 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7543 (tp30)
  outliers start: 46
  outliers final: 29
  residues processed: 192
  average time/residue: 0.2310
  time to fit residues: 63.1442
Evaluate side-chains
  187 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 150
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  419 PHE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.148581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108836 restraints weight = 15054.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.09
r_work: 0.3114 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11941  Z= 0.139
  Angle     :  0.547   7.389  16293  Z= 0.285
  Chirality :  0.040   0.165   1881
  Planarity :  0.004   0.064   1962
  Dihedral  :  4.436  53.738   1541
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.46 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 26.78 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  1.90 (0.22), residues: 1476
  helix:  1.92 (0.16), residues: 1110
  sheet:  None (None), residues: 0
  loop : -0.79 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 329 
 HIS   0.003   0.001   HIS B 192 
 PHE   0.029   0.001   PHE A 332 
 TYR   0.018   0.001   TYR C 154 
 ARG   0.003   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  854)
  hydrogen bonds       : angle       4.07063 ( 2547)
  covalent geometry    : bond        0.00325 (11940)
  covalent geometry    : angle       0.54725 (16293)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 157
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 TRP cc_start: 0.7355 (m-10) cc_final: 0.7135 (m-90)
REVERT: A  185 ARG cc_start: 0.6914 (ttm110) cc_final: 0.6669 (ttp-110)
REVERT: A  447 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7391 (mmm160)
REVERT: A  481 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7708 (m-80)
REVERT: A  483 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7469 (p)
REVERT: B   30 LEU cc_start: 0.8843 (tp) cc_final: 0.8567 (mp)
REVERT: B   99 MET cc_start: 0.8237 (ttt) cc_final: 0.7886 (ptm)
REVERT: B  185 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6575 (mtp85)
REVERT: B  429 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7492 (tt)
REVERT: B  481 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7765 (m-80)
REVERT: C   38 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6606 (tppt)
REVERT: C   91 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6477 (t80)
REVERT: C   99 MET cc_start: 0.8258 (ttt) cc_final: 0.7654 (ttt)
REVERT: C  156 MET cc_start: 0.7975 (mmm) cc_final: 0.7624 (mmm)
REVERT: C  228 GLU cc_start: 0.6804 (pt0) cc_final: 0.6432 (pm20)
REVERT: C  481 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8085 (m-80)
REVERT: C  499 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7544 (tp30)
  outliers start: 52
  outliers final: 32
  residues processed: 190
  average time/residue: 0.2478
  time to fit residues: 66.6490
Evaluate side-chains
  195 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 155
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  417 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 137 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.149634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.109971 restraints weight = 15089.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.09
r_work: 0.3121 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11941  Z= 0.124
  Angle     :  0.533   7.868  16293  Z= 0.277
  Chirality :  0.039   0.166   1881
  Planarity :  0.004   0.063   1962
  Dihedral  :  4.360  52.487   1541
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.52 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 26.95 %
    Favored  : 69.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  2.00 (0.22), residues: 1476
  helix:  1.99 (0.16), residues: 1110
  sheet:  None (None), residues: 0
  loop : -0.74 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 329 
 HIS   0.002   0.000   HIS B 192 
 PHE   0.028   0.001   PHE A 332 
 TYR   0.019   0.001   TYR C 154 
 ARG   0.004   0.000   ARG C  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  854)
  hydrogen bonds       : angle       4.00744 ( 2547)
  covalent geometry    : bond        0.00283 (11940)
  covalent geometry    : angle       0.53314 (16293)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 161
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8969 (tp) cc_final: 0.8624 (mt)
REVERT: A   42 TRP cc_start: 0.7385 (m-10) cc_final: 0.7140 (m-90)
REVERT: A  144 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8652 (tp)
REVERT: A  185 ARG cc_start: 0.6921 (ttm110) cc_final: 0.6670 (ttp-110)
REVERT: A  447 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7338 (mmm160)
REVERT: A  481 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7716 (m-80)
REVERT: A  483 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7454 (p)
REVERT: B   30 LEU cc_start: 0.8853 (tp) cc_final: 0.8567 (mp)
REVERT: B   99 MET cc_start: 0.8216 (ttt) cc_final: 0.7872 (ptm)
REVERT: B  185 ARG cc_start: 0.7080 (ttp-110) cc_final: 0.6590 (mtp85)
REVERT: B  218 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8452 (m)
REVERT: B  316 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8274 (m-40)
REVERT: B  429 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7476 (tt)
REVERT: B  481 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7695 (m-80)
REVERT: C   38 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6546 (tppt)
REVERT: C   99 MET cc_start: 0.8222 (ttt) cc_final: 0.7694 (ttt)
REVERT: C  228 GLU cc_start: 0.6769 (pt0) cc_final: 0.6200 (pm20)
REVERT: C  481 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8043 (m-80)
REVERT: C  499 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7561 (tp30)
  outliers start: 49
  outliers final: 35
  residues processed: 192
  average time/residue: 0.2243
  time to fit residues: 62.8593
Evaluate side-chains
  200 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 155
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  419 PHE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  417 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 142 optimal weight:    3.9990
   chunk 125 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 144 optimal weight:    0.7980
   chunk 123 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.150175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109080 restraints weight = 15130.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.14
r_work: 0.3123 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11941  Z= 0.129
  Angle     :  0.545   9.725  16293  Z= 0.281
  Chirality :  0.040   0.165   1881
  Planarity :  0.004   0.062   1962
  Dihedral  :  4.339  51.760   1541
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.46 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 26.95 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  1.99 (0.22), residues: 1476
  helix:  2.00 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -0.83 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 329 
 HIS   0.002   0.001   HIS B 192 
 PHE   0.028   0.001   PHE A 332 
 TYR   0.018   0.001   TYR C 154 
 ARG   0.005   0.000   ARG C  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  854)
  hydrogen bonds       : angle       4.00572 ( 2547)
  covalent geometry    : bond        0.00299 (11940)
  covalent geometry    : angle       0.54460 (16293)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 160
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8949 (tp) cc_final: 0.8644 (mt)
REVERT: A   42 TRP cc_start: 0.7433 (m-10) cc_final: 0.7207 (m-90)
REVERT: A  185 ARG cc_start: 0.6964 (ttm110) cc_final: 0.6738 (ttp-110)
REVERT: A  447 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7300 (mmm160)
REVERT: A  481 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7808 (m-80)
REVERT: A  483 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7476 (p)
REVERT: B   30 LEU cc_start: 0.8864 (tp) cc_final: 0.8571 (mp)
REVERT: B   99 MET cc_start: 0.8206 (ttt) cc_final: 0.7874 (ptm)
REVERT: B  185 ARG cc_start: 0.7089 (ttp-110) cc_final: 0.6603 (mtp85)
REVERT: B  218 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8457 (m)
REVERT: B  429 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7490 (tt)
REVERT: B  481 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7735 (m-80)
REVERT: C   38 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6520 (tppt)
REVERT: C   91 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6564 (t80)
REVERT: C  228 GLU cc_start: 0.6823 (pt0) cc_final: 0.6236 (pm20)
REVERT: C  481 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8016 (m-80)
REVERT: C  499 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7548 (tp30)
  outliers start: 52
  outliers final: 35
  residues processed: 192
  average time/residue: 0.2400
  time to fit residues: 65.5963
Evaluate side-chains
  199 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 155
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  417 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 115 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0770
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 122 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.149998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.110484 restraints weight = 14925.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.08
r_work: 0.3134 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11941  Z= 0.127
  Angle     :  0.548  11.124  16293  Z= 0.282
  Chirality :  0.040   0.166   1881
  Planarity :  0.004   0.062   1962
  Dihedral  :  4.321  50.975   1541
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.95 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  2.00 (0.22), residues: 1476
  helix:  2.01 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -0.83 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 329 
 HIS   0.003   0.001   HIS B 192 
 PHE   0.037   0.001   PHE B 420 
 TYR   0.020   0.001   TYR C 154 
 ARG   0.005   0.000   ARG C  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03628 (  854)
  hydrogen bonds       : angle       4.00009 ( 2547)
  covalent geometry    : bond        0.00293 (11940)
  covalent geometry    : angle       0.54775 (16293)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 159
  time to evaluate  : 1.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8918 (tp) cc_final: 0.8619 (mt)
REVERT: A   74 PHE cc_start: 0.7572 (m-10) cc_final: 0.7334 (m-10)
REVERT: A  144 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8715 (tp)
REVERT: A  181 PHE cc_start: 0.7191 (t80) cc_final: 0.6601 (t80)
REVERT: A  185 ARG cc_start: 0.6933 (ttm110) cc_final: 0.6669 (mtm110)
REVERT: A  447 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7331 (mmm160)
REVERT: A  481 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7951 (m-80)
REVERT: B   30 LEU cc_start: 0.8841 (tp) cc_final: 0.8545 (mp)
REVERT: B   99 MET cc_start: 0.8118 (ttt) cc_final: 0.7820 (ptm)
REVERT: B  185 ARG cc_start: 0.7022 (ttp-110) cc_final: 0.6552 (mtp85)
REVERT: B  218 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8561 (m)
REVERT: B  429 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7547 (tt)
REVERT: B  481 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7828 (m-80)
REVERT: C   38 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6448 (tppt)
REVERT: C   91 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6423 (t80)
REVERT: C  228 GLU cc_start: 0.6995 (pt0) cc_final: 0.6359 (pm20)
REVERT: C  238 ILE cc_start: 0.7541 (mm) cc_final: 0.7337 (mm)
REVERT: C  481 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8093 (m-80)
REVERT: C  499 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7592 (tp30)
  outliers start: 50
  outliers final: 36
  residues processed: 191
  average time/residue: 0.3137
  time to fit residues: 87.0044
Evaluate side-chains
  202 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 157
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  417 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 133 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 116 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.149895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110454 restraints weight = 14838.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.07
r_work: 0.3130 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11941  Z= 0.130
  Angle     :  0.545  11.402  16293  Z= 0.282
  Chirality :  0.040   0.166   1881
  Planarity :  0.004   0.062   1962
  Dihedral  :  4.321  50.737   1541
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 27.68 %
    Favored  : 68.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  2.02 (0.22), residues: 1476
  helix:  2.01 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -0.81 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 329 
 HIS   0.002   0.001   HIS B 192 
 PHE   0.038   0.001   PHE B 420 
 TYR   0.020   0.001   TYR C 154 
 ARG   0.005   0.001   ARG C  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  854)
  hydrogen bonds       : angle       4.00622 ( 2547)
  covalent geometry    : bond        0.00302 (11940)
  covalent geometry    : angle       0.54538 (16293)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 1.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8916 (tp) cc_final: 0.8617 (mt)
REVERT: A   74 PHE cc_start: 0.7630 (m-10) cc_final: 0.7408 (m-10)
REVERT: A  181 PHE cc_start: 0.7264 (t80) cc_final: 0.6752 (t80)
REVERT: A  185 ARG cc_start: 0.6984 (ttm110) cc_final: 0.6652 (mtm110)
REVERT: A  195 ASP cc_start: 0.8484 (m-30) cc_final: 0.8176 (m-30)
REVERT: A  447 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7352 (mmm160)
REVERT: A  481 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7978 (m-80)
REVERT: A  483 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7605 (p)
REVERT: B   30 LEU cc_start: 0.8841 (tp) cc_final: 0.8542 (mp)
REVERT: B   99 MET cc_start: 0.8119 (ttt) cc_final: 0.7835 (ptm)
REVERT: B  218 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (m)
REVERT: B  429 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7531 (tt)
REVERT: B  481 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7754 (m-80)
REVERT: C   38 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6442 (tppt)
REVERT: C   91 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6339 (t80)
REVERT: C   99 MET cc_start: 0.8162 (ttt) cc_final: 0.7690 (ttt)
REVERT: C  228 GLU cc_start: 0.7013 (pt0) cc_final: 0.6380 (pm20)
REVERT: C  238 ILE cc_start: 0.7542 (mm) cc_final: 0.7341 (mm)
REVERT: C  481 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8136 (m-80)
REVERT: C  499 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7581 (tp30)
  outliers start: 45
  outliers final: 33
  residues processed: 183
  average time/residue: 0.3257
  time to fit residues: 89.5796
Evaluate side-chains
  198 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 156
  time to evaluate  : 1.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 CYS
Chi-restraints excluded: chain A residue   91 PHE
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  481 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  402 PHE
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  442 SER
Chi-restraints excluded: chain B residue  481 PHE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   91 PHE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  128 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  383 MET
Chi-restraints excluded: chain C residue  417 PHE
Chi-restraints excluded: chain C residue  481 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  499 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0030
   chunk 47 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 136 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 112 optimal weight:    0.6980
   chunk 134 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.4590

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.152373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111511 restraints weight = 15031.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.18
r_work: 0.3155 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11941  Z= 0.114
  Angle     :  0.523   6.654  16293  Z= 0.272
  Chirality :  0.039   0.168   1881
  Planarity :  0.004   0.061   1962
  Dihedral  :  4.229  49.848   1541
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 27.85 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.49 %
    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:  2.14 (0.22), residues: 1476
  helix:  2.12 (0.16), residues: 1101
  sheet:  None (None), residues: 0
  loop : -0.72 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 329 
 HIS   0.003   0.001   HIS B 192 
 PHE   0.036   0.001   PHE B 420 
 TYR   0.019   0.001   TYR C 154 
 ARG   0.004   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03484 (  854)
  hydrogen bonds       : angle       3.95015 ( 2547)
  covalent geometry    : bond        0.00254 (11940)
  covalent geometry    : angle       0.52332 (16293)
  Misc. bond           : bond        0.00000 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6763.09 seconds
wall clock time: 120 minutes 27.94 seconds (7227.94 seconds total)