Starting phenix.real_space_refine
on Thu Feb  5 04:41:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zh8_74225/02_2026/9zh8_74225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zh8_74225/02_2026/9zh8_74225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zh8_74225/02_2026/9zh8_74225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zh8_74225/02_2026/9zh8_74225.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zh8_74225/02_2026/9zh8_74225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zh8_74225/02_2026/9zh8_74225.map"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.088
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      40      5.16       5
     C    9056      2.51       5
     N    2540      2.21       5
     O    3283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14919
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3568
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
      Conformer: "B"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
          bond proxies already assigned to first conformer: 3628
    Chain: "B"
      Number of atoms: 3568
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
      Conformer: "B"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
          bond proxies already assigned to first conformer: 3628
    Chain: "C"
      Number of atoms: 3568
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
      Conformer: "B"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
          bond proxies already assigned to first conformer: 3628
    Chain: "D"
      Number of atoms: 3568
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
      Conformer: "B"
        Number of residues, atoms: 477, 3560
          Classifications: {'peptide': 477}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 444}
          bond proxies already assigned to first conformer: 3628
    Chain: "A"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 163
          Classifications: {'water': 163}
          Link IDs: {None: 162}
    Chain: "B"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 162
          Classifications: {'water': 162}
          Link IDs: {None: 161}
    Chain: "C"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 161
          Classifications: {'water': 161}
          Link IDs: {None: 160}
    Chain: "D"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 161
          Classifications: {'water': 161}
          Link IDs: {None: 160}
  Time building chain proxies: 5.93, per 1000 atoms: 0.40
  Number of scatterers: 14919
  At special positions: 0
  Unit cell: (98.494, 96.866, 105.006, 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      40     16.00
     O    3283      8.00
     N    2540      7.00
     C    9056      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3464

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 18 sheets defined
      45.7% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 64
      removed outlier: 3.785A  pdb=" N   LYS A  64 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 84
    Processing helix  chain 'A' and resid 84 through 97
    Processing helix  chain 'A' and resid 99 through 122
      removed outlier: 3.885A  pdb=" N   ARG A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 172
      removed outlier: 4.322A  pdb=" N   LYS A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 197
      removed outlier: 3.601A  pdb=" N   PHE A 194 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'A' and resid 232 through 246
    Processing helix  chain 'A' and resid 267 through 280
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 299 through 313
    Processing helix  chain 'A' and resid 331 through 348
      removed outlier: 3.776A  pdb=" N   LEU A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 382
    Processing helix  chain 'A' and resid 397 through 406
    Processing helix  chain 'A' and resid 420 through 431
    Processing helix  chain 'A' and resid 463 through 469
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'B' and resid 44 through 64
      removed outlier: 3.784A  pdb=" N   LYS B  64 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 84
    Processing helix  chain 'B' and resid 84 through 97
    Processing helix  chain 'B' and resid 99 through 122
      removed outlier: 3.886A  pdb=" N   ARG B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 172
      removed outlier: 4.322A  pdb=" N   LYS B 164 " --> pdb=" O   GLN B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 197
      removed outlier: 3.602A  pdb=" N   PHE B 194 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 219
    Processing helix  chain 'B' and resid 232 through 246
    Processing helix  chain 'B' and resid 267 through 280
    Processing helix  chain 'B' and resid 281 through 285
    Processing helix  chain 'B' and resid 299 through 313
    Processing helix  chain 'B' and resid 331 through 348
      removed outlier: 3.777A  pdb=" N   LEU B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 382
    Processing helix  chain 'B' and resid 397 through 406
    Processing helix  chain 'B' and resid 420 through 431
    Processing helix  chain 'B' and resid 463 through 469
      Proline residue:  B 469  - end of helix
    Processing helix  chain 'C' and resid 44 through 64
      removed outlier: 3.784A  pdb=" N   LYS C  64 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 84
    Processing helix  chain 'C' and resid 84 through 97
    Processing helix  chain 'C' and resid 99 through 122
      removed outlier: 3.886A  pdb=" N   ARG C 122 " --> pdb=" O   ALA C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 172
      removed outlier: 4.321A  pdb=" N   LYS C 164 " --> pdb=" O   GLN C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 197
      removed outlier: 3.602A  pdb=" N   PHE C 194 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 219
    Processing helix  chain 'C' and resid 232 through 246
    Processing helix  chain 'C' and resid 267 through 280
    Processing helix  chain 'C' and resid 281 through 285
    Processing helix  chain 'C' and resid 299 through 313
    Processing helix  chain 'C' and resid 331 through 348
      removed outlier: 3.776A  pdb=" N   LEU C 335 " --> pdb=" O   ASN C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 382
    Processing helix  chain 'C' and resid 397 through 406
    Processing helix  chain 'C' and resid 420 through 431
    Processing helix  chain 'C' and resid 463 through 469
      Proline residue:  C 469  - end of helix
    Processing helix  chain 'D' and resid 44 through 64
      removed outlier: 3.784A  pdb=" N   LYS D  64 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 84
    Processing helix  chain 'D' and resid 84 through 97
    Processing helix  chain 'D' and resid 99 through 122
      removed outlier: 3.885A  pdb=" N   ARG D 122 " --> pdb=" O   ALA D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 172
      removed outlier: 4.321A  pdb=" N   LYS D 164 " --> pdb=" O   GLN D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 197
      removed outlier: 3.602A  pdb=" N   PHE D 194 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 219
    Processing helix  chain 'D' and resid 232 through 246
    Processing helix  chain 'D' and resid 267 through 280
    Processing helix  chain 'D' and resid 281 through 285
    Processing helix  chain 'D' and resid 299 through 313
    Processing helix  chain 'D' and resid 331 through 348
      removed outlier: 3.776A  pdb=" N   LEU D 335 " --> pdb=" O   ASN D 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 382
    Processing helix  chain 'D' and resid 397 through 406
    Processing helix  chain 'D' and resid 420 through 431
    Processing helix  chain 'D' and resid 463 through 469
      Proline residue:  D 469  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 29
      removed outlier: 6.245A  pdb=" N   ILE A  26 " --> pdb=" O   LYS A  39 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS A  39 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL A  28 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 354
      removed outlier: 6.470A  pdb=" N   VAL B 370 " --> pdb=" O   GLU B 353 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   THR B 291 " --> pdb=" O   VAL B 389 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA B 258 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   LEU B 294 " --> pdb=" O   ALA B 258 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL B 260 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   HIS B 296 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   VAL B 262 " --> pdb=" O   HIS B 296 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   PHE B 417 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE B 261 " --> pdb=" O   PHE B 417 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   LEU B 436 " --> pdb=" O   THR A 473 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   SER A 475 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ILE B 438 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR A 477 " --> pdb=" O   ILE B 438 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLN A 138 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLN C 138 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   LEU D 436 " --> pdb=" O   THR C 473 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   SER C 475 " --> pdb=" O   LEU D 436 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ILE D 438 " --> pdb=" O   SER C 475 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   THR C 477 " --> pdb=" O   ILE D 438 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   PHE D 417 " --> pdb=" O   PRO D 259 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE D 261 " --> pdb=" O   PHE D 417 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA D 258 " --> pdb=" O   ARG D 292 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   LEU D 294 " --> pdb=" O   ALA D 258 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   VAL D 260 " --> pdb=" O   LEU D 294 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   HIS D 296 " --> pdb=" O   VAL D 260 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   VAL D 262 " --> pdb=" O   HIS D 296 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   THR D 291 " --> pdb=" O   VAL D 389 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL D 370 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 207
      removed outlier: 6.165A  pdb=" N   VAL A 148 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   LYS A 178 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA A 150 " --> pdb=" O   LYS A 178 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 354
      removed outlier: 6.470A  pdb=" N   VAL A 370 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   THR A 291 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ALA A 258 " --> pdb=" O   ARG A 292 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   LEU A 294 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   VAL A 260 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   HIS A 296 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   VAL A 262 " --> pdb=" O   HIS A 296 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   PHE A 417 " --> pdb=" O   PRO A 259 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE A 261 " --> pdb=" O   PHE A 417 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLN B 138 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   GLN D 138 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   PHE C 417 " --> pdb=" O   PRO C 259 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE C 261 " --> pdb=" O   PHE C 417 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ALA C 258 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   LEU C 294 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   VAL C 260 " --> pdb=" O   LEU C 294 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   HIS C 296 " --> pdb=" O   VAL C 260 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   VAL C 262 " --> pdb=" O   HIS C 296 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   THR C 291 " --> pdb=" O   VAL C 389 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL C 370 " --> pdb=" O   GLU C 353 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 411
    Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 13
    Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 29
      removed outlier: 6.245A  pdb=" N   ILE B  26 " --> pdb=" O   LYS B  39 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS B  39 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL B  28 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 207
      removed outlier: 6.165A  pdb=" N   VAL B 148 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   LYS B 178 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ALA B 150 " --> pdb=" O   LYS B 178 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 410 through 411
    Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 13
    Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 29
      removed outlier: 6.245A  pdb=" N   ILE C  26 " --> pdb=" O   LYS C  39 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS C  39 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL C  28 " --> pdb=" O   ILE C  37 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 207
      removed outlier: 6.165A  pdb=" N   VAL C 148 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   LYS C 178 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA C 150 " --> pdb=" O   LYS C 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 410 through 411
    Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 13
    Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 29
      removed outlier: 6.245A  pdb=" N   ILE D  26 " --> pdb=" O   LYS D  39 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LYS D  39 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL D  28 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 204 through 207
      removed outlier: 6.165A  pdb=" N   VAL D 148 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   LYS D 178 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA D 150 " --> pdb=" O   LYS D 178 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 410 through 411

    800 hydrogen bonds defined for protein.
    2252 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.96

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4859
        1.34 -     1.46: 2935
        1.46 -     1.58: 6718
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 14584
  Sorted by residual:
  bond pdb=" CA  GLY A 209 "
       pdb=" C   GLY A 209 "
    ideal  model  delta    sigma   weight residual
    1.524  1.512  0.012 1.20e-02 6.94e+03 1.01e+00
  bond pdb=" CA  GLY D 209 "
       pdb=" C   GLY D 209 "
    ideal  model  delta    sigma   weight residual
    1.524  1.512  0.011 1.20e-02 6.94e+03 9.15e-01
  bond pdb=" CA  GLY C 209 "
       pdb=" C   GLY C 209 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.20e-02 6.94e+03 8.71e-01
  bond pdb=" CA  GLY B 209 "
       pdb=" C   GLY B 209 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.20e-02 6.94e+03 8.20e-01
  bond pdb=" C   TYR A 208 "
       pdb=" N   GLY A 209 "
    ideal  model  delta    sigma   weight residual
    1.319  1.329 -0.010 1.44e-02 4.82e+03 4.70e-01
  ... (remaining 14579 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 19285
        1.05 -     2.10: 424
        2.10 -     3.15: 129
        3.15 -     4.20: 19
        4.20 -     5.25: 15
  Bond angle restraints: 19872
  Sorted by residual:
  angle pdb=" N   GLY D 209 "
        pdb=" CA  GLY D 209 "
        pdb=" C   GLY D 209 "
      ideal   model   delta    sigma   weight residual
     110.20  113.00   -2.80 1.32e+00 5.74e-01 4.50e+00
  angle pdb=" N   GLY C 209 "
        pdb=" CA  GLY C 209 "
        pdb=" C   GLY C 209 "
      ideal   model   delta    sigma   weight residual
     110.20  112.99   -2.79 1.32e+00 5.74e-01 4.46e+00
  angle pdb=" N   GLY B 209 "
        pdb=" CA  GLY B 209 "
        pdb=" C   GLY B 209 "
      ideal   model   delta    sigma   weight residual
     110.20  112.99   -2.79 1.32e+00 5.74e-01 4.45e+00
  angle pdb=" N   GLY A 209 "
        pdb=" CA  GLY A 209 "
        pdb=" C   GLY A 209 "
      ideal   model   delta    sigma   weight residual
     110.20  112.97   -2.77 1.32e+00 5.74e-01 4.42e+00
  angle pdb=" CB  MET A 338 "
        pdb=" CG  MET A 338 "
        pdb=" SD  MET A 338 "
      ideal   model   delta    sigma   weight residual
     112.70  117.95   -5.25 3.00e+00 1.11e-01 3.07e+00
  ... (remaining 19867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 7833
       17.04 -    34.07: 651
       34.07 -    51.11: 168
       51.11 -    68.15: 88
       68.15 -    85.18: 20
  Dihedral angle restraints: 8760
    sinusoidal: 3356
      harmonic: 5404
  Sorted by residual:
  dihedral pdb=" CA  GLN C 429 "
           pdb=" C   GLN C 429 "
           pdb=" N   ARG C 430 "
           pdb=" CA  ARG C 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.28  -16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  GLN B 429 "
           pdb=" C   GLN B 429 "
           pdb=" N   ARG B 430 "
           pdb=" CA  ARG B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.29  -16.71     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  GLN D 429 "
           pdb=" C   GLN D 429 "
           pdb=" N   ARG D 430 "
           pdb=" CA  ARG D 430 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.29  -16.71     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 8757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1317
       0.026 -    0.051: 532
       0.051 -    0.077: 200
       0.077 -    0.102: 138
       0.102 -    0.128: 81
  Chirality restraints: 2268
  Sorted by residual:
  chirality pdb=" CA  ILE A  26 "
            pdb=" N   ILE A  26 "
            pdb=" C   ILE A  26 "
            pdb=" CB  ILE A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  VAL C 140 "
            pdb=" N   VAL C 140 "
            pdb=" C   VAL C 140 "
            pdb=" CB  VAL C 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 2265 not shown)

  Planarity restraints: 2632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 219 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO D 220 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO D 220 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 220 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 219 "   -0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO B 220 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 220 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 220 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 219 "    0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO A 220 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.018 5.00e-02 4.00e+02
  ... (remaining 2629 not shown)

  Histogram of nonbonded interaction distances:
        2.65 -     3.10: 10789
        3.10 -     3.55: 16539
        3.55 -     4.00: 28061
        4.00 -     4.45: 32487
        4.45 -     4.90: 46844
  Nonbonded interactions: 134720
  Sorted by model distance:
  nonbonded pdb=" N   ILE B  37 "
            pdb=" N   GLY B  38 "
     model   vdw
     2.649 2.560
  nonbonded pdb=" N   ILE D  37 "
            pdb=" N   GLY D  38 "
     model   vdw
     2.649 2.560
  nonbonded pdb=" N   ILE A  37 "
            pdb=" N   GLY A  38 "
     model   vdw
     2.649 2.560
  nonbonded pdb=" N   ILE C  37 "
            pdb=" N   GLY C  38 "
     model   vdw
     2.650 2.560
  nonbonded pdb=" N   GLN A 440 "
            pdb=" O   GLN A 440 "
     model   vdw
     2.655 2.496
  ... (remaining 134715 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'
  selection = chain 'D'
}

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=0.50 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:             1.550
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.390
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:7.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  14584  Z= 0.083
  Angle     :  0.439   5.253  19872  Z= 0.225
  Chirality :  0.041   0.128   2268
  Planarity :  0.004   0.031   2632
  Dihedral  : 15.652  85.183   5296
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.01 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.18), residues: 1904
  helix:  0.59 (0.16), residues: 816
  sheet:  0.40 (0.27), residues: 364
  loop :  0.63 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 358 
 TYR   0.004   0.001   TYR B 208 
 PHE   0.011   0.001   PHE C 175 
 TRP   0.008   0.001   TRP D 116 
 HIS   0.002   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 (14584)
  covalent geometry    : angle       0.43948 (19872)
  hydrogen bonds       : bond        0.21646 (  800)
  hydrogen bonds       : angle       7.25092 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.588 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8182 (mttm) cc_final: 0.7889 (mmtp)
REVERT: A  309 LYS cc_start: 0.8759 (mttp) cc_final: 0.8144 (mppt)
REVERT: A  315 LYS cc_start: 0.8753 (tptm) cc_final: 0.8420 (tptp)
REVERT: A  381 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8045 (m-80)
REVERT: A  386 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7933 (t80)
REVERT: A  399 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7568 (pm20)
REVERT: B  213 GLU cc_start: 0.9055 (tt0) cc_final: 0.8836 (tt0)
REVERT: B  309 LYS cc_start: 0.8687 (mttp) cc_final: 0.8084 (mppt)
REVERT: B  315 LYS cc_start: 0.8601 (tptm) cc_final: 0.8257 (tptp)
REVERT: B  381 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7716 (m-80)
REVERT: B  386 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7984 (t80)
REVERT: B  399 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7628 (pm20)
REVERT: C  213 GLU cc_start: 0.9046 (tt0) cc_final: 0.8825 (tt0)
REVERT: C  305 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8289 (mtt90)
REVERT: C  309 LYS cc_start: 0.8698 (mttp) cc_final: 0.8109 (mppt)
REVERT: C  315 LYS cc_start: 0.8612 (tptm) cc_final: 0.8267 (tptp)
REVERT: C  381 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7635 (m-80)
REVERT: C  386 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7994 (t80)
REVERT: C  399 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7624 (pm20)
REVERT: D  213 GLU cc_start: 0.9046 (tt0) cc_final: 0.8824 (tt0)
REVERT: D  309 LYS cc_start: 0.8702 (mttp) cc_final: 0.8112 (mppt)
REVERT: D  315 LYS cc_start: 0.8674 (tptm) cc_final: 0.8293 (tptp)
REVERT: D  381 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.7625 (m-80)
REVERT: D  386 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7986 (t80)
REVERT: D  399 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7617 (pm20)
  outliers start: 19
  outliers final: 5
  residues processed: 159
  average time/residue: 0.9701
  time to fit residues: 164.2881
Evaluate side-chains
  157 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  321 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  386 PHE
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  386 PHE
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  386 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 245 GLN
C 245 GLN
D 245 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.101214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.089214 restraints weight = 26912.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 0.90
r_work: 0.2743 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9004
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  14584  Z= 0.203
  Angle     :  0.625   6.161  19872  Z= 0.338
  Chirality :  0.048   0.136   2268
  Planarity :  0.006   0.039   2632
  Dihedral  :  6.817  56.168   2095
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.62 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.19), residues: 1904
  helix:  1.47 (0.18), residues: 820
  sheet: -0.11 (0.27), residues: 368
  loop :  0.61 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  75 
 TYR   0.009   0.002   TYR B 470 
 PHE   0.013   0.003   PHE D 175 
 TRP   0.013   0.002   TRP A 116 
 HIS   0.006   0.002   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (14584)
  covalent geometry    : angle       0.62528 (19872)
  hydrogen bonds       : bond        0.07357 (  800)
  hydrogen bonds       : angle       5.38182 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.615 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8642 (mttp) cc_final: 0.8133 (mppt)
REVERT: A  315 LYS cc_start: 0.8655 (tptm) cc_final: 0.8392 (tptp)
REVERT: A  381 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.7933 (m-80)
REVERT: A  386 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.7936 (t80)
REVERT: B  213 GLU cc_start: 0.8673 (tt0) cc_final: 0.8470 (tt0)
REVERT: B  309 LYS cc_start: 0.8581 (mttp) cc_final: 0.8088 (mppt)
REVERT: B  315 LYS cc_start: 0.8623 (tptm) cc_final: 0.8345 (tptp)
REVERT: B  381 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7788 (m-80)
REVERT: B  386 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7936 (t80)
REVERT: B  399 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7658 (pm20)
REVERT: C  213 GLU cc_start: 0.8671 (tt0) cc_final: 0.8465 (tt0)
REVERT: C  309 LYS cc_start: 0.8593 (mttp) cc_final: 0.8096 (mppt)
REVERT: C  315 LYS cc_start: 0.8619 (tptm) cc_final: 0.8335 (tptp)
REVERT: C  381 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.7792 (m-80)
REVERT: C  386 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7936 (t80)
REVERT: D  213 GLU cc_start: 0.8683 (tt0) cc_final: 0.8478 (tt0)
REVERT: D  309 LYS cc_start: 0.8580 (mttp) cc_final: 0.8082 (mppt)
REVERT: D  315 LYS cc_start: 0.8628 (tptm) cc_final: 0.8355 (tptp)
REVERT: D  381 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7796 (m-80)
REVERT: D  386 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7920 (t80)
  outliers start: 35
  outliers final: 16
  residues processed: 180
  average time/residue: 0.9296
  time to fit residues: 178.9193
Evaluate side-chains
  175 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  386 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  386 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  386 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 60 optimal weight:    8.9990
   chunk 176 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 181 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 156 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 118 optimal weight:    6.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
B 155 ASN
C 155 ASN
D 155 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.101257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.089879 restraints weight = 31165.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 0.93
r_work: 0.2742 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9013
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  14584  Z= 0.200
  Angle     :  0.614   5.565  19872  Z= 0.334
  Chirality :  0.047   0.136   2268
  Planarity :  0.006   0.043   2632
  Dihedral  :  6.787  56.439   2092
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 10.62 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.19), residues: 1904
  helix:  1.66 (0.18), residues: 820
  sheet: -0.18 (0.27), residues: 372
  loop :  0.58 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 249 
 TYR   0.009   0.002   TYR C 470 
 PHE   0.013   0.003   PHE B 175 
 TRP   0.014   0.002   TRP D 116 
 HIS   0.006   0.002   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (14584)
  covalent geometry    : angle       0.61429 (19872)
  hydrogen bonds       : bond        0.07178 (  800)
  hydrogen bonds       : angle       5.32207 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8679 (mttp) cc_final: 0.8167 (mppt)
REVERT: A  315 LYS cc_start: 0.8683 (tptm) cc_final: 0.8421 (tptp)
REVERT: A  381 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.7858 (m-80)
REVERT: B  309 LYS cc_start: 0.8635 (mttp) cc_final: 0.8129 (mppt)
REVERT: B  315 LYS cc_start: 0.8664 (tptm) cc_final: 0.8403 (tptp)
REVERT: B  381 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7891 (m-80)
REVERT: C  309 LYS cc_start: 0.8654 (mttp) cc_final: 0.8144 (mppt)
REVERT: C  315 LYS cc_start: 0.8657 (tptm) cc_final: 0.8396 (tptp)
REVERT: C  381 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.7890 (m-80)
REVERT: D  309 LYS cc_start: 0.8638 (mttp) cc_final: 0.8131 (mppt)
REVERT: D  315 LYS cc_start: 0.8660 (tptm) cc_final: 0.8401 (tptp)
REVERT: D  381 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.7894 (m-80)
  outliers start: 37
  outliers final: 19
  residues processed: 182
  average time/residue: 0.9437
  time to fit residues: 183.5617
Evaluate side-chains
  174 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   chunk 151 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 108 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 150 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 166 optimal weight:    3.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3021 r_free = 0.3021 target = 0.101680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.090438 restraints weight = 30322.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 0.90
r_work: 0.2752 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9008
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  14584  Z= 0.193
  Angle     :  0.604   5.505  19872  Z= 0.328
  Chirality :  0.047   0.135   2268
  Planarity :  0.006   0.044   2632
  Dihedral  :  6.246  56.324   2084
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.60 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.20), residues: 1904
  helix:  1.71 (0.18), residues: 820
  sheet: -0.20 (0.27), residues: 372
  loop :  0.57 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  75 
 TYR   0.009   0.002   TYR C 470 
 PHE   0.013   0.003   PHE B 175 
 TRP   0.014   0.002   TRP D 116 
 HIS   0.006   0.002   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (14584)
  covalent geometry    : angle       0.60428 (19872)
  hydrogen bonds       : bond        0.06931 (  800)
  hydrogen bonds       : angle       5.25713 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8672 (mttp) cc_final: 0.8167 (mppt)
REVERT: A  315 LYS cc_start: 0.8661 (tptm) cc_final: 0.8409 (tptp)
REVERT: A  381 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.7867 (m-80)
REVERT: B  309 LYS cc_start: 0.8657 (mttp) cc_final: 0.8160 (mppt)
REVERT: B  315 LYS cc_start: 0.8672 (tptm) cc_final: 0.8417 (tptp)
REVERT: B  381 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.7887 (m-80)
REVERT: C  309 LYS cc_start: 0.8665 (mttp) cc_final: 0.8173 (mppt)
REVERT: C  315 LYS cc_start: 0.8665 (tptm) cc_final: 0.8411 (tptp)
REVERT: C  381 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.7884 (m-80)
REVERT: D  309 LYS cc_start: 0.8659 (mttp) cc_final: 0.8158 (mppt)
REVERT: D  315 LYS cc_start: 0.8674 (tptm) cc_final: 0.8420 (tptp)
REVERT: D  381 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.7885 (m-80)
  outliers start: 31
  outliers final: 20
  residues processed: 179
  average time/residue: 0.9384
  time to fit residues: 179.6326
Evaluate side-chains
  176 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 113 optimal weight:    0.3980
   chunk 104 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 161 optimal weight:    8.9990
   chunk 126 optimal weight:    3.9990
   chunk 166 optimal weight:    2.9990
   chunk 116 optimal weight:    9.9990
   chunk 129 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.4788

-------------------------------------------------------------------------------
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 = 0.3033 r_free = 0.3033 target = 0.102512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.090545 restraints weight = 27226.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 0.90
r_work: 0.2760 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2653
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8991
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  14584  Z= 0.172
  Angle     :  0.576   5.528  19872  Z= 0.312
  Chirality :  0.046   0.134   2268
  Planarity :  0.005   0.043   2632
  Dihedral  :  6.147  56.362   2084
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.22 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.20), residues: 1904
  helix:  1.80 (0.18), residues: 820
  sheet: -0.15 (0.27), residues: 372
  loop :  0.60 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  75 
 TYR   0.008   0.002   TYR C 470 
 PHE   0.012   0.002   PHE B 175 
 TRP   0.014   0.002   TRP D 116 
 HIS   0.005   0.002   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14584)
  covalent geometry    : angle       0.57639 (19872)
  hydrogen bonds       : bond        0.06518 (  800)
  hydrogen bonds       : angle       5.16756 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8654 (mttp) cc_final: 0.8135 (mppt)
REVERT: A  315 LYS cc_start: 0.8644 (tptm) cc_final: 0.8387 (tptp)
REVERT: A  381 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7851 (m-80)
REVERT: B  309 LYS cc_start: 0.8635 (mttp) cc_final: 0.8131 (mppt)
REVERT: B  315 LYS cc_start: 0.8648 (tptm) cc_final: 0.8395 (tptp)
REVERT: B  381 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7860 (m-80)
REVERT: C  309 LYS cc_start: 0.8651 (mttp) cc_final: 0.8148 (mppt)
REVERT: C  315 LYS cc_start: 0.8635 (tptm) cc_final: 0.8382 (tptp)
REVERT: C  381 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7857 (m-80)
REVERT: D  309 LYS cc_start: 0.8642 (mttp) cc_final: 0.8131 (mppt)
REVERT: D  315 LYS cc_start: 0.8648 (tptm) cc_final: 0.8392 (tptp)
REVERT: D  381 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7858 (m-80)
  outliers start: 28
  outliers final: 15
  residues processed: 178
  average time/residue: 0.9262
  time to fit residues: 176.2584
Evaluate side-chains
  172 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   chunk 125 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3012 r_free = 0.3012 target = 0.101114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.089713 restraints weight = 28779.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 0.90
r_work: 0.2742 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090  14584  Z= 0.216
  Angle     :  0.632   5.836  19872  Z= 0.344
  Chirality :  0.048   0.135   2268
  Planarity :  0.006   0.044   2632
  Dihedral  :  6.343  56.180   2084
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.64 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.20), residues: 1904
  helix:  1.69 (0.18), residues: 820
  sheet: -0.23 (0.27), residues: 372
  loop :  0.55 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  75 
 TYR   0.011   0.002   TYR C 470 
 PHE   0.014   0.003   PHE A 175 
 TRP   0.013   0.003   TRP C 116 
 HIS   0.007   0.002   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (14584)
  covalent geometry    : angle       0.63216 (19872)
  hydrogen bonds       : bond        0.07318 (  800)
  hydrogen bonds       : angle       5.32600 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8670 (mttp) cc_final: 0.8144 (mppt)
REVERT: A  315 LYS cc_start: 0.8683 (tptm) cc_final: 0.8431 (tptp)
REVERT: A  381 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7878 (m-80)
REVERT: B  309 LYS cc_start: 0.8672 (mttp) cc_final: 0.8154 (mppt)
REVERT: B  315 LYS cc_start: 0.8676 (tptm) cc_final: 0.8420 (tptp)
REVERT: B  381 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7883 (m-80)
REVERT: C  309 LYS cc_start: 0.8686 (mttp) cc_final: 0.8166 (mppt)
REVERT: C  315 LYS cc_start: 0.8664 (tptm) cc_final: 0.8411 (tptp)
REVERT: C  381 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.7880 (m-80)
REVERT: D  309 LYS cc_start: 0.8675 (mttp) cc_final: 0.8150 (mppt)
REVERT: D  315 LYS cc_start: 0.8676 (tptm) cc_final: 0.8422 (tptp)
REVERT: D  381 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.7881 (m-80)
  outliers start: 29
  outliers final: 20
  residues processed: 176
  average time/residue: 0.9490
  time to fit residues: 178.7460
Evaluate side-chains
  173 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  162 VAL
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 129 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 148 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 157 optimal weight:    2.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.3030 r_free = 0.3030 target = 0.102298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.090920 restraints weight = 28740.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 0.90
r_work: 0.2756 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2653
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8998
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  14584  Z= 0.182
  Angle     :  0.588   5.822  19872  Z= 0.319
  Chirality :  0.046   0.134   2268
  Planarity :  0.005   0.043   2632
  Dihedral  :  6.211  56.290   2084
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.19 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.20), residues: 1904
  helix:  1.77 (0.18), residues: 820
  sheet: -0.17 (0.28), residues: 372
  loop :  0.58 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  75 
 TYR   0.008   0.002   TYR B 470 
 PHE   0.013   0.003   PHE A 175 
 TRP   0.014   0.002   TRP C 116 
 HIS   0.005   0.002   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (14584)
  covalent geometry    : angle       0.58844 (19872)
  hydrogen bonds       : bond        0.06692 (  800)
  hydrogen bonds       : angle       5.20752 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8671 (mttp) cc_final: 0.8154 (mppt)
REVERT: A  315 LYS cc_start: 0.8658 (tptm) cc_final: 0.8413 (tptp)
REVERT: A  381 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7863 (m-80)
REVERT: B  309 LYS cc_start: 0.8660 (mttp) cc_final: 0.8150 (mppt)
REVERT: B  315 LYS cc_start: 0.8657 (tptm) cc_final: 0.8408 (tptp)
REVERT: B  381 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: C  309 LYS cc_start: 0.8678 (mttp) cc_final: 0.8170 (mppt)
REVERT: C  315 LYS cc_start: 0.8642 (tptm) cc_final: 0.8393 (tptp)
REVERT: C  381 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.7865 (m-80)
REVERT: D  309 LYS cc_start: 0.8668 (mttp) cc_final: 0.8154 (mppt)
REVERT: D  315 LYS cc_start: 0.8657 (tptm) cc_final: 0.8408 (tptp)
REVERT: D  381 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.7868 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 173
  average time/residue: 0.9507
  time to fit residues: 175.8240
Evaluate side-chains
  171 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 137 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 135 optimal weight:   10.0000
   chunk 169 optimal weight:    6.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3031 r_free = 0.3031 target = 0.102371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.090580 restraints weight = 35385.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 1.03
r_work: 0.2750 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9007
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  14584  Z= 0.177
  Angle     :  0.584   5.920  19872  Z= 0.316
  Chirality :  0.046   0.134   2268
  Planarity :  0.005   0.043   2632
  Dihedral  :  6.193  56.307   2084
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.26 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.20), residues: 1904
  helix:  1.80 (0.18), residues: 820
  sheet: -0.16 (0.28), residues: 372
  loop :  0.58 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 249 
 TYR   0.008   0.002   TYR D 470 
 PHE   0.013   0.003   PHE A 175 
 TRP   0.014   0.002   TRP D 116 
 HIS   0.006   0.002   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (14584)
  covalent geometry    : angle       0.58447 (19872)
  hydrogen bonds       : bond        0.06631 (  800)
  hydrogen bonds       : angle       5.18977 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8682 (mttp) cc_final: 0.8155 (mppt)
REVERT: A  315 LYS cc_start: 0.8665 (tptm) cc_final: 0.8416 (tptp)
REVERT: A  381 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: B  309 LYS cc_start: 0.8678 (mttp) cc_final: 0.8163 (mppt)
REVERT: B  315 LYS cc_start: 0.8669 (tptm) cc_final: 0.8415 (tptp)
REVERT: B  381 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.7874 (m-80)
REVERT: C  309 LYS cc_start: 0.8698 (mttp) cc_final: 0.8179 (mppt)
REVERT: C  315 LYS cc_start: 0.8653 (tptm) cc_final: 0.8400 (tptp)
REVERT: C  381 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: D  309 LYS cc_start: 0.8690 (mttp) cc_final: 0.8165 (mppt)
REVERT: D  315 LYS cc_start: 0.8667 (tptm) cc_final: 0.8412 (tptp)
REVERT: D  381 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7872 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 173
  average time/residue: 0.9510
  time to fit residues: 175.7465
Evaluate side-chains
  172 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 176 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 172 optimal weight:    8.9990
   chunk 182 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3046 r_free = 0.3046 target = 0.103452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.092093 restraints weight = 23004.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 0.80
r_work: 0.2795 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 2.25 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8968
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14584  Z= 0.154
  Angle     :  0.554   5.872  19872  Z= 0.298
  Chirality :  0.045   0.135   2268
  Planarity :  0.005   0.042   2632
  Dihedral  :  6.051  56.442   2084
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.47 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.20), residues: 1904
  helix:  1.92 (0.18), residues: 816
  sheet: -0.09 (0.28), residues: 372
  loop :  0.56 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  75 
 TYR   0.007   0.002   TYR B 470 
 PHE   0.012   0.002   PHE A 175 
 TRP   0.014   0.002   TRP D 116 
 HIS   0.005   0.002   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (14584)
  covalent geometry    : angle       0.55394 (19872)
  hydrogen bonds       : bond        0.06121 (  800)
  hydrogen bonds       : angle       5.07871 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8654 (mttp) cc_final: 0.8126 (mppt)
REVERT: A  315 LYS cc_start: 0.8626 (tptm) cc_final: 0.8381 (tptp)
REVERT: A  381 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.7824 (m-80)
REVERT: B  309 LYS cc_start: 0.8628 (mttp) cc_final: 0.8117 (mppt)
REVERT: B  315 LYS cc_start: 0.8633 (tptm) cc_final: 0.8385 (tptp)
REVERT: B  381 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7825 (m-80)
REVERT: C  309 LYS cc_start: 0.8645 (mttp) cc_final: 0.8129 (mppt)
REVERT: C  315 LYS cc_start: 0.8616 (tptm) cc_final: 0.8371 (tptp)
REVERT: C  381 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7822 (m-80)
REVERT: D  309 LYS cc_start: 0.8635 (mttp) cc_final: 0.8115 (mppt)
REVERT: D  315 LYS cc_start: 0.8631 (tptm) cc_final: 0.8381 (tptp)
REVERT: D  381 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.7824 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 175
  average time/residue: 0.9385
  time to fit residues: 175.4469
Evaluate side-chains
  176 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  159 ASN
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  159 ASN
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 187 optimal weight:    0.0980
   chunk 124 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 119 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 155 optimal weight:   10.0000
   chunk 162 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3112 r_free = 0.3112 target = 0.108083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.096646 restraints weight = 30085.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 0.93
r_work: 0.2846 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8924
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  14584  Z= 0.111
  Angle     :  0.485   5.636  19872  Z= 0.258
  Chirality :  0.043   0.136   2268
  Planarity :  0.004   0.038   2632
  Dihedral  :  5.625  56.535   2084
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.75 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.20), residues: 1904
  helix:  2.25 (0.18), residues: 804
  sheet:  0.10 (0.28), residues: 372
  loop :  0.58 (0.24), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 334 
 TYR   0.007   0.001   TYR A 208 
 PHE   0.011   0.001   PHE B 175 
 TRP   0.016   0.001   TRP B 116 
 HIS   0.003   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (14584)
  covalent geometry    : angle       0.48490 (19872)
  hydrogen bonds       : bond        0.04731 (  800)
  hydrogen bonds       : angle       4.74052 ( 2252)

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

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

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3808 Ramachandran restraints generated.
    1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.582 
Fit side-chains
REVERT: A  309 LYS cc_start: 0.8635 (mttp) cc_final: 0.8110 (mppt)
REVERT: A  315 LYS cc_start: 0.8561 (tptm) cc_final: 0.8308 (tptp)
REVERT: A  347 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7451 (mttp)
REVERT: A  381 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7824 (m-80)
REVERT: B  309 LYS cc_start: 0.8618 (mttp) cc_final: 0.8103 (mppt)
REVERT: B  315 LYS cc_start: 0.8550 (tptm) cc_final: 0.8308 (tptp)
REVERT: B  347 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7459 (mttp)
REVERT: B  381 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7826 (m-80)
REVERT: C  309 LYS cc_start: 0.8630 (mttp) cc_final: 0.8118 (mppt)
REVERT: C  315 LYS cc_start: 0.8545 (tptm) cc_final: 0.8303 (tptp)
REVERT: C  347 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7453 (mttp)
REVERT: C  381 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7828 (m-80)
REVERT: D  309 LYS cc_start: 0.8637 (mttp) cc_final: 0.8118 (mppt)
REVERT: D  315 LYS cc_start: 0.8567 (tptm) cc_final: 0.8323 (tptp)
REVERT: D  347 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7453 (mttp)
REVERT: D  381 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7824 (m-80)
REVERT: D  455 ASP cc_start: 0.9011 (m-30) cc_final: 0.8801 (m-30)
  outliers start: 20
  outliers final: 9
  residues processed: 171
  average time/residue: 0.9456
  time to fit residues: 172.9858
Evaluate side-chains
  166 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  381 PHE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  381 PHE
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain D residue  279 LYS
Chi-restraints excluded: chain D residue  377 GLU
Chi-restraints excluded: chain D residue  381 PHE
Chi-restraints excluded: chain D residue  481 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 139 optimal weight:    0.9990
   chunk 185 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 137 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 170 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 135 optimal weight:    7.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3089 r_free = 0.3089 target = 0.106471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.094517 restraints weight = 26969.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 0.90
r_work: 0.2826 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 2.49 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14584  Z= 0.122
  Angle     :  0.501   5.733  19872  Z= 0.267
  Chirality :  0.043   0.136   2268
  Planarity :  0.005   0.040   2632
  Dihedral  :  5.684  56.875   2084
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 14.24 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.20), residues: 1904
  helix:  2.27 (0.18), residues: 804
  sheet:  0.07 (0.28), residues: 372
  loop :  0.59 (0.24), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  82 
 TYR   0.007   0.001   TYR A 208 
 PHE   0.011   0.002   PHE B 175 
 TRP   0.015   0.002   TRP C 116 
 HIS   0.004   0.002   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (14584)
  covalent geometry    : angle       0.50109 (19872)
  hydrogen bonds       : bond        0.05197 (  800)
  hydrogen bonds       : angle       4.78572 ( 2252)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5819.29 seconds
wall clock time: 100 minutes 5.66 seconds (6005.66 seconds total)