Starting phenix.real_space_refine
on Tue Jan 13 21:49:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f1z_31425/01_2026/7f1z_31425.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f1z_31425/01_2026/7f1z_31425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f1z_31425/01_2026/7f1z_31425.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f1z_31425/01_2026/7f1z_31425.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f1z_31425/01_2026/7f1z_31425.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f1z_31425/01_2026/7f1z_31425.map"
  }
  resolution = 3.46
  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=  -0.001 sd=   0.122
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3063 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      47      5.16       5
     C    4604      2.51       5
     N    1272      2.21       5
     O    1326      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7251
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 2208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2208
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 9, 'TRANS': 267}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1941
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 2624
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 434
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP B  27 " occ=0.45
      ... (14 atoms not shown)
      pdb=" OD2BASP B  27 " occ=0.55
  Time building chain proxies: 2.15, per 1000 atoms: 0.30
  Number of scatterers: 7251
  At special positions: 0
  Unit cell: (78.264, 97.83, 123.918, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P       2     15.00
     O    1326      8.00
     N    1272      7.00
     C    4604      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 357.7 milliseconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1736

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      50.2% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'F' and resid 20 through 51
      removed outlier: 3.602A  pdb=" N   PHE F  51 " --> pdb=" O   ALA F  47 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 56
      removed outlier: 3.616A  pdb=" N   ARG F  55 " --> pdb=" O   PHE F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  79  - end of helix
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.333A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ILE F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER F 127 " --> pdb=" O   TRP F 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
    Processing helix  chain 'F' and resid 136 through 161
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
      removed outlier: 3.744A  pdb=" N   ILE F 196 " --> pdb=" O   ARG F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 203 through 237
    Processing helix  chain 'F' and resid 265 through 299
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.890A  pdb=" N   SER F 324 " --> pdb=" O   GLY F 320 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER F 325 " --> pdb=" O   TRP F 321 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'A' and resid 13 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.603A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.890A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'D' and resid 55 through 59
      removed outlier: 3.533A  pdb=" N   ASN D  59 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 9.510A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.769A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.683A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.770A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.810A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.624A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.686A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.830A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.332A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2174
        1.33 -     1.45: 1279
        1.45 -     1.57: 3886
        1.57 -     1.69: 3
        1.69 -     1.81: 64
  Bond restraints: 7406
  Sorted by residual:
  bond pdb=" C   TRP B  99 "
       pdb=" N   VAL B 100 "
    ideal  model  delta    sigma   weight residual
    1.334  1.274  0.060 1.29e-02 6.01e+03 2.18e+01
  bond pdb=" CB  VAL F  77 "
       pdb=" CG1 VAL F  77 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.46e+00
  bond pdb=" CB  VAL F 116 "
       pdb=" CG1 VAL F 116 "
    ideal  model  delta    sigma   weight residual
    1.521  1.432  0.089 3.30e-02 9.18e+02 7.25e+00
  bond pdb=" CB  ASN F 327 "
       pdb=" CG  ASN F 327 "
    ideal  model  delta    sigma   weight residual
    1.516  1.451  0.065 2.50e-02 1.60e+03 6.68e+00
  bond pdb=" CG1 ILE F 111 "
       pdb=" CD1 ILE F 111 "
    ideal  model  delta    sigma   weight residual
    1.513  1.413  0.100 3.90e-02 6.57e+02 6.51e+00
  ... (remaining 7401 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 9472
        2.27 -     4.54: 484
        4.54 -     6.82: 69
        6.82 -     9.09: 14
        9.09 -    11.36: 3
  Bond angle restraints: 10042
  Sorted by residual:
  angle pdb=" C   GLY A 226 "
        pdb=" N   GLN A 227 "
        pdb=" CA  GLN A 227 "
      ideal   model   delta    sigma   weight residual
     123.32  113.08   10.24 1.88e+00 2.83e-01 2.97e+01
  angle pdb=" N   GLY A 355 "
        pdb=" CA  GLY A 355 "
        pdb=" C   GLY A 355 "
      ideal   model   delta    sigma   weight residual
     115.62  106.74    8.88 1.71e+00 3.42e-01 2.70e+01
  angle pdb=" C   LYS A 233 "
        pdb=" N   TRP A 234 "
        pdb=" CA  TRP A 234 "
      ideal   model   delta    sigma   weight residual
     121.58  113.11    8.47 1.95e+00 2.63e-01 1.89e+01
  angle pdb=" N   ARG A 283 "
        pdb=" CA  ARG A 283 "
        pdb=" C   ARG A 283 "
      ideal   model   delta    sigma   weight residual
     113.88  108.67    5.21 1.23e+00 6.61e-01 1.79e+01
  angle pdb=" N   CYS F  96 "
        pdb=" CA  CYS F  96 "
        pdb=" C   CYS F  96 "
      ideal   model   delta    sigma   weight residual
     112.54  107.60    4.94 1.22e+00 6.72e-01 1.64e+01
  ... (remaining 10037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.73: 3753
       15.73 -    31.45: 508
       31.45 -    47.18: 114
       47.18 -    62.90: 20
       62.90 -    78.63: 9
  Dihedral angle restraints: 4404
    sinusoidal: 1734
      harmonic: 2670
  Sorted by residual:
  dihedral pdb=" CA  PHE F  95 "
           pdb=" C   PHE F  95 "
           pdb=" N   CYS F  96 "
           pdb=" CA  CYS F  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.52  -24.48     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CB  CYS F  96 "
           pdb=" SG  CYS F  96 "
           pdb=" SG  CYS F 186 "
           pdb=" CB  CYS F 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.66  -33.66     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" C4' GDP A 401 "
           pdb=" O5' GDP A 401 "
           pdb=" C5' GDP A 401 "
           pdb=" PA  GDP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.02  110.45   69.57     1      2.00e+01 2.50e-03 1.56e+01
  ... (remaining 4401 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 897
       0.075 -    0.150: 211
       0.150 -    0.225: 23
       0.225 -    0.300: 2
       0.300 -    0.375: 1
  Chirality restraints: 1134
  Sorted by residual:
  chirality pdb=" CB  VAL F 119 "
            pdb=" CA  VAL F 119 "
            pdb=" CG1 VAL F 119 "
            pdb=" CG2 VAL F 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.38 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" CB  ILE F 330 "
            pdb=" CA  ILE F 330 "
            pdb=" CG1 ILE F 330 "
            pdb=" CG2 ILE F 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CB  ILE F 329 "
            pdb=" CA  ILE F 329 "
            pdb=" CG1 ILE F 329 "
            pdb=" CG2 ILE F 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1131 not shown)

  Planarity restraints: 1271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 104 "    0.040 2.00e-02 2.50e+03   8.04e-02 6.46e+01
        pdb=" C   ILE F 104 "   -0.139 2.00e-02 2.50e+03
        pdb=" O   ILE F 104 "    0.051 2.00e-02 2.50e+03
        pdb=" N   MET F 105 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F  94 "    0.027 2.00e-02 2.50e+03   5.40e-02 2.92e+01
        pdb=" C   SER F  94 "   -0.093 2.00e-02 2.50e+03
        pdb=" O   SER F  94 "    0.035 2.00e-02 2.50e+03
        pdb=" N   PHE F  95 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 347 "   -0.025 2.00e-02 2.50e+03   4.98e-02 2.48e+01
        pdb=" C   ARG A 347 "    0.086 2.00e-02 2.50e+03
        pdb=" O   ARG A 347 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   ILE A 348 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 1268 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 117
        2.60 -     3.18: 6728
        3.18 -     3.75: 11469
        3.75 -     4.33: 15999
        4.33 -     4.90: 26136
  Nonbonded interactions: 60449
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.025 3.040
  nonbonded pdb=" O   HIS B  54 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.055 3.040
  nonbonded pdb=" O   HIS F 164 "
            pdb=" N   SER F 191 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" OG  SER A  54 "
            pdb=" O1B GDP A 401 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" NE2 HIS A 362 "
            pdb=" OD2 ASP A 378 "
     model   vdw
     2.142 3.120
  ... (remaining 60444 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.38 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:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
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      :  0.012   0.100   7407  Z= 0.542
  Angle     :  1.149  11.361  10044  Z= 0.663
  Chirality :  0.062   0.375   1134
  Planarity :  0.008   0.091   1271
  Dihedral  : 15.178  78.629   2665
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 18.98
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.26 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 10.77 %
    Favored  : 88.46 %
  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: -2.39 (0.24), residues: 900
  helix: -1.65 (0.21), residues: 410
  sheet: -0.97 (0.34), residues: 191
  loop : -1.53 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 197 
 TYR   0.020   0.003   TYR A 360 
 PHE   0.043   0.003   PHE F 333 
 TRP   0.014   0.003   TRP F 148 
 HIS   0.006   0.002   HIS F 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.01240 ( 7406)
  covalent geometry    : angle       1.14827 (10042)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       3.56197 (    2)
  hydrogen bonds       : bond        0.15177 (  413)
  hydrogen bonds       : angle       7.22033 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 153
  time to evaluate  : 0.281 
Fit side-chains
REVERT: F   85 GLU cc_start: 0.8109 (tp30) cc_final: 0.7866 (tp30)
REVERT: F   86 ILE cc_start: 0.8673 (mm) cc_final: 0.8417 (mt)
REVERT: F  278 MET cc_start: 0.8061 (mmm) cc_final: 0.7803 (mmt)
REVERT: A   35 GLN cc_start: 0.8256 (tp40) cc_final: 0.7757 (pt0)
REVERT: B   57 LYS cc_start: 0.8108 (mttp) cc_final: 0.7826 (ptpp)
REVERT: B  111 TYR cc_start: 0.8452 (m-80) cc_final: 0.8099 (m-80)
REVERT: B  134 ARG cc_start: 0.5156 (tpm170) cc_final: 0.4719 (tpm170)
  outliers start: 5
  outliers final: 3
  residues processed: 157
  average time/residue: 0.0923
  time to fit residues: 19.2257
Evaluate side-chains
  122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  206 PRO
Chi-restraints excluded: chain A residue  223 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 334 ASN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 HIS
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
D  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.216878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.158461 restraints weight = 16632.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 4.41
r_work: 0.3201 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7407  Z= 0.162
  Angle     :  0.665  11.726  10044  Z= 0.344
  Chirality :  0.046   0.171   1134
  Planarity :  0.005   0.039   1271
  Dihedral  :  5.571  71.729   1019
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.67 %
    Favored  : 80.26 %
  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: -0.55 (0.26), residues: 900
  helix:  0.23 (0.23), residues: 403
  sheet: -0.30 (0.36), residues: 181
  loop : -1.01 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 197 
 TYR   0.009   0.001   TYR B 264 
 PHE   0.013   0.001   PHE F 288 
 TRP   0.022   0.002   TRP B 297 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7406)
  covalent geometry    : angle       0.66473 (10042)
  SS BOND              : bond        0.00313 (    1)
  SS BOND              : angle       1.21800 (    2)
  hydrogen bonds       : bond        0.05295 (  413)
  hydrogen bonds       : angle       5.19148 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.275 
Fit side-chains
REVERT: F   35 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8036 (mm)
REVERT: F   55 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.6283 (tpt170)
REVERT: F   85 GLU cc_start: 0.8108 (tp30) cc_final: 0.6870 (tp30)
REVERT: A   61 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8175 (mtp180)
REVERT: A  209 GLU cc_start: 0.7268 (tt0) cc_final: 0.6820 (tt0)
REVERT: B   57 LYS cc_start: 0.8259 (mttp) cc_final: 0.7518 (ptpp)
REVERT: B   59 TYR cc_start: 0.8763 (m-80) cc_final: 0.8498 (m-80)
REVERT: B  111 TYR cc_start: 0.8710 (m-80) cc_final: 0.8250 (m-80)
REVERT: B  134 ARG cc_start: 0.4810 (tpm170) cc_final: 0.4421 (tpm170)
REVERT: B  217 MET cc_start: 0.7347 (tpt) cc_final: 0.6487 (mtm)
REVERT: B  262 MET cc_start: 0.6372 (ttm) cc_final: 0.5982 (ttm)
REVERT: B  323 ASP cc_start: 0.7595 (p0) cc_final: 0.7148 (p0)
REVERT: B  325 MET cc_start: 0.7917 (mmt) cc_final: 0.7448 (mmp)
  outliers start: 23
  outliers final: 12
  residues processed: 156
  average time/residue: 0.0781
  time to fit residues: 16.9272
Evaluate side-chains
  135 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  186 CYS
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  336 ASP
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain D residue   59 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 23 optimal weight:    0.3980
   chunk 55 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0040
   chunk 32 optimal weight:    8.9990
   chunk 49 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 78 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
A 294 GLN
B 225 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.222934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.177244 restraints weight = 23996.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 5.02
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3892 r_free = 0.3892    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3891 r_free = 0.3891    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7407  Z= 0.125
  Angle     :  0.597  13.133  10044  Z= 0.303
  Chirality :  0.044   0.169   1134
  Planarity :  0.004   0.043   1271
  Dihedral  :  5.087  68.109   1012
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.21 %
    Favored  : 78.46 %
  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:  0.28 (0.27), residues: 900
  helix:  1.19 (0.25), residues: 397
  sheet: -0.18 (0.36), residues: 192
  loop : -0.79 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 197 
 TYR   0.008   0.001   TYR B 124 
 PHE   0.023   0.001   PHE A 315 
 TRP   0.020   0.002   TRP B 211 
 HIS   0.007   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7406)
  covalent geometry    : angle       0.59647 (10042)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       1.11368 (    2)
  hydrogen bonds       : bond        0.04485 (  413)
  hydrogen bonds       : angle       4.77987 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  209 GLU cc_start: 0.6559 (tt0) cc_final: 0.6351 (tt0)
REVERT: B  101 MET cc_start: 0.8151 (mtp) cc_final: 0.7899 (mtp)
REVERT: B  111 TYR cc_start: 0.8388 (m-80) cc_final: 0.7901 (m-80)
REVERT: B  134 ARG cc_start: 0.4658 (tpm170) cc_final: 0.4187 (tpm170)
  outliers start: 25
  outliers final: 13
  residues processed: 140
  average time/residue: 0.0779
  time to fit residues: 15.1913
Evaluate side-chains
  122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  114 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.219348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.164697 restraints weight = 15389.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 3.66
r_work: 0.3285 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7407  Z= 0.187
  Angle     :  0.633  11.936  10044  Z= 0.325
  Chirality :  0.045   0.173   1134
  Planarity :  0.004   0.044   1271
  Dihedral  :  5.080  66.615   1012
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.49 %
    Favored  : 76.15 %
  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:  0.43 (0.27), residues: 900
  helix:  1.35 (0.25), residues: 400
  sheet: -0.13 (0.37), residues: 171
  loop : -0.73 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 219 
 TYR   0.009   0.001   TYR F 122 
 PHE   0.021   0.002   PHE B 180 
 TRP   0.020   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 7406)
  covalent geometry    : angle       0.63313 (10042)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       1.30102 (    2)
  hydrogen bonds       : bond        0.04852 (  413)
  hydrogen bonds       : angle       4.80046 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.288 
Fit side-chains
REVERT: F   76 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7252 (mp)
REVERT: A  209 GLU cc_start: 0.7367 (tt0) cc_final: 0.6990 (tt0)
REVERT: B   57 LYS cc_start: 0.8217 (mttp) cc_final: 0.7607 (ptpp)
REVERT: B   59 TYR cc_start: 0.8790 (m-80) cc_final: 0.8580 (m-80)
REVERT: B  101 MET cc_start: 0.8541 (mtp) cc_final: 0.8321 (mtp)
REVERT: B  111 TYR cc_start: 0.8743 (m-80) cc_final: 0.8226 (m-80)
REVERT: B  134 ARG cc_start: 0.5026 (tpm170) cc_final: 0.4457 (tpm170)
REVERT: B  212 ASP cc_start: 0.6646 (p0) cc_final: 0.6209 (p0)
REVERT: B  220 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6117 (mp10)
REVERT: B  323 ASP cc_start: 0.7843 (p0) cc_final: 0.7198 (p0)
REVERT: B  325 MET cc_start: 0.8166 (mmp) cc_final: 0.7265 (mtt)
  outliers start: 33
  outliers final: 21
  residues processed: 137
  average time/residue: 0.0775
  time to fit residues: 14.8852
Evaluate side-chains
  134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  112 LEU
Chi-restraints excluded: chain F residue  115 CYS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  186 CYS
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  294 ILE
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 68 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.220797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.163138 restraints weight = 21120.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 5.05
r_work: 0.3229 rms_B_bonded: 5.04 restraints_weight: 2.0000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7407  Z= 0.145
  Angle     :  0.590  12.637  10044  Z= 0.301
  Chirality :  0.044   0.150   1134
  Planarity :  0.004   0.044   1271
  Dihedral  :  4.991  64.845   1012
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 20.51 %
    Favored  : 74.49 %
  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:  0.59 (0.27), residues: 900
  helix:  1.45 (0.25), residues: 400
  sheet: -0.00 (0.37), residues: 163
  loop : -0.63 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 197 
 TYR   0.008   0.001   TYR B 264 
 PHE   0.016   0.001   PHE B 180 
 TRP   0.022   0.002   TRP B 211 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7406)
  covalent geometry    : angle       0.59018 (10042)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       1.08243 (    2)
  hydrogen bonds       : bond        0.04472 (  413)
  hydrogen bonds       : angle       4.67652 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 0.305 
Fit side-chains
REVERT: F   29 PHE cc_start: 0.6428 (t80) cc_final: 0.6206 (t80)
REVERT: A  209 GLU cc_start: 0.7306 (tt0) cc_final: 0.6753 (tt0)
REVERT: B  111 TYR cc_start: 0.8771 (m-80) cc_final: 0.8222 (m-80)
REVERT: B  134 ARG cc_start: 0.5091 (tpm170) cc_final: 0.4534 (tpm170)
REVERT: B  170 ASP cc_start: 0.6437 (p0) cc_final: 0.5677 (t0)
REVERT: B  212 ASP cc_start: 0.6701 (p0) cc_final: 0.6397 (p0)
REVERT: B  217 MET cc_start: 0.6718 (ptt) cc_final: 0.6449 (ptt)
REVERT: B  220 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.5977 (mp10)
REVERT: B  234 PHE cc_start: 0.5060 (OUTLIER) cc_final: 0.4562 (t80)
REVERT: B  323 ASP cc_start: 0.7657 (p0) cc_final: 0.7029 (p0)
REVERT: B  325 MET cc_start: 0.8513 (mmp) cc_final: 0.7541 (mtt)
  outliers start: 39
  outliers final: 25
  residues processed: 132
  average time/residue: 0.0759
  time to fit residues: 14.0875
Evaluate side-chains
  128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  115 CYS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  186 CYS
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain D residue   59 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 28 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0000
   chunk 46 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
D  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.218848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.160976 restraints weight = 21802.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 4.93
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3765 r_free = 0.3765    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3765 r_free = 0.3765    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7407  Z= 0.156
  Angle     :  0.592  12.371  10044  Z= 0.302
  Chirality :  0.044   0.151   1134
  Planarity :  0.004   0.045   1271
  Dihedral  :  4.953  62.877   1012
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 21.41 %
    Favored  : 74.23 %
  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:  0.57 (0.27), residues: 900
  helix:  1.43 (0.25), residues: 402
  sheet: -0.05 (0.37), residues: 169
  loop : -0.62 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 197 
 TYR   0.010   0.001   TYR B 264 
 PHE   0.020   0.001   PHE B 241 
 TRP   0.021   0.002   TRP B 211 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7406)
  covalent geometry    : angle       0.59205 (10042)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       1.17405 (    2)
  hydrogen bonds       : bond        0.04537 (  413)
  hydrogen bonds       : angle       4.67645 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.264 
Fit side-chains
REVERT: F   29 PHE cc_start: 0.6579 (t80) cc_final: 0.6336 (t80)
REVERT: A  209 GLU cc_start: 0.6994 (tt0) cc_final: 0.6545 (tt0)
REVERT: B   57 LYS cc_start: 0.8030 (mttp) cc_final: 0.7375 (ptpp)
REVERT: B  111 TYR cc_start: 0.8512 (m-80) cc_final: 0.7988 (m-80)
REVERT: B  134 ARG cc_start: 0.4976 (tpm170) cc_final: 0.4432 (tpm170)
REVERT: B  220 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6670 (mp10)
REVERT: B  234 PHE cc_start: 0.5982 (OUTLIER) cc_final: 0.5258 (t80)
REVERT: B  323 ASP cc_start: 0.7485 (p0) cc_final: 0.6833 (p0)
REVERT: B  325 MET cc_start: 0.7626 (mmp) cc_final: 0.7401 (mtt)
  outliers start: 34
  outliers final: 27
  residues processed: 133
  average time/residue: 0.0788
  time to fit residues: 14.7573
Evaluate side-chains
  140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  112 LEU
Chi-restraints excluded: chain F residue  115 CYS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain D residue   59 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 11 optimal weight:    0.0970
   chunk 47 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
F 113 ASN
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.221604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.161103 restraints weight = 18967.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 4.76
r_work: 0.3244 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7407  Z= 0.118
  Angle     :  0.569  13.002  10044  Z= 0.286
  Chirality :  0.043   0.168   1134
  Planarity :  0.004   0.045   1271
  Dihedral  :  4.870  62.175   1012
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 21.67 %
    Favored  : 74.10 %
  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:  0.68 (0.27), residues: 900
  helix:  1.56 (0.25), residues: 400
  sheet:  0.04 (0.36), residues: 168
  loop : -0.62 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 197 
 TYR   0.008   0.001   TYR A 253 
 PHE   0.015   0.001   PHE B 180 
 TRP   0.024   0.002   TRP B 211 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7406)
  covalent geometry    : angle       0.56867 (10042)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       0.91572 (    2)
  hydrogen bonds       : bond        0.04158 (  413)
  hydrogen bonds       : angle       4.57858 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  209 GLU cc_start: 0.7020 (tt0) cc_final: 0.6625 (tt0)
REVERT: B  111 TYR cc_start: 0.8716 (m-80) cc_final: 0.8169 (m-80)
REVERT: B  134 ARG cc_start: 0.5044 (tpm170) cc_final: 0.4479 (tpm170)
REVERT: B  170 ASP cc_start: 0.6304 (p0) cc_final: 0.5678 (t0)
REVERT: B  212 ASP cc_start: 0.7117 (p0) cc_final: 0.5763 (p0)
REVERT: B  220 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6195 (mp10)
REVERT: B  307 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8314 (t)
REVERT: B  323 ASP cc_start: 0.7601 (p0) cc_final: 0.7045 (p0)
REVERT: B  325 MET cc_start: 0.8554 (mmp) cc_final: 0.7422 (mtt)
REVERT: B  339 TRP cc_start: 0.7811 (OUTLIER) cc_final: 0.7320 (m100)
  outliers start: 33
  outliers final: 18
  residues processed: 130
  average time/residue: 0.0786
  time to fit residues: 14.2413
Evaluate side-chains
  123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  112 LEU
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 73 optimal weight:   20.0000
   chunk 52 optimal weight:   30.0000
   chunk 27 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.220880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.165325 restraints weight = 21732.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 5.00
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7407  Z= 0.145
  Angle     :  0.590  12.147  10044  Z= 0.298
  Chirality :  0.044   0.202   1134
  Planarity :  0.004   0.050   1271
  Dihedral  :  4.910  59.353   1012
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.05 %
    Favored  : 73.85 %
  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:  0.69 (0.28), residues: 900
  helix:  1.56 (0.25), residues: 399
  sheet: -0.03 (0.36), residues: 171
  loop : -0.55 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 197 
 TYR   0.009   0.001   TYR A 253 
 PHE   0.020   0.001   PHE B 292 
 TRP   0.021   0.001   TRP B 211 
 HIS   0.010   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7406)
  covalent geometry    : angle       0.58977 (10042)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       1.01092 (    2)
  hydrogen bonds       : bond        0.04342 (  413)
  hydrogen bonds       : angle       4.63895 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: F   29 PHE cc_start: 0.6586 (t80) cc_final: 0.6372 (t80)
REVERT: F   76 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7293 (mp)
REVERT: A  209 GLU cc_start: 0.6718 (tt0) cc_final: 0.6283 (tt0)
REVERT: B  111 TYR cc_start: 0.8510 (m-80) cc_final: 0.7947 (m-80)
REVERT: B  134 ARG cc_start: 0.5113 (tpm170) cc_final: 0.4601 (tpm170)
REVERT: B  212 ASP cc_start: 0.6750 (p0) cc_final: 0.6111 (p0)
REVERT: B  220 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6782 (mp10)
REVERT: B  323 ASP cc_start: 0.7582 (p0) cc_final: 0.6936 (p0)
REVERT: B  325 MET cc_start: 0.7652 (mmp) cc_final: 0.7304 (mtt)
REVERT: B  339 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.7165 (m100)
  outliers start: 32
  outliers final: 22
  residues processed: 135
  average time/residue: 0.0757
  time to fit residues: 14.5250
Evaluate side-chains
  133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  112 LEU
Chi-restraints excluded: chain F residue  115 CYS
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  278 MET
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  294 ILE
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0170
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
D  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.223103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.165921 restraints weight = 16221.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 3.89
r_work: 0.3313 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7407  Z= 0.120
  Angle     :  0.589  12.986  10044  Z= 0.291
  Chirality :  0.044   0.231   1134
  Planarity :  0.004   0.052   1271
  Dihedral  :  4.831  58.377   1012
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.46 %
    Favored  : 73.33 %
  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:  0.75 (0.28), residues: 900
  helix:  1.64 (0.25), residues: 400
  sheet: -0.01 (0.37), residues: 172
  loop : -0.58 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 197 
 TYR   0.009   0.001   TYR A 253 
 PHE   0.019   0.001   PHE B 292 
 TRP   0.022   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7406)
  covalent geometry    : angle       0.58878 (10042)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.86487 (    2)
  hydrogen bonds       : bond        0.04008 (  413)
  hydrogen bonds       : angle       4.53737 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.294 
Fit side-chains
REVERT: F   42 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8873 (p)
REVERT: F   96 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6464 (t)
REVERT: A   50 ASN cc_start: 0.8070 (t0) cc_final: 0.7242 (t0)
REVERT: A  209 GLU cc_start: 0.6867 (tt0) cc_final: 0.6470 (tt0)
REVERT: B  111 TYR cc_start: 0.8742 (m-80) cc_final: 0.8140 (m-80)
REVERT: B  134 ARG cc_start: 0.5085 (tpm170) cc_final: 0.4545 (tpm170)
REVERT: B  212 ASP cc_start: 0.6992 (p0) cc_final: 0.6247 (p0)
REVERT: B  220 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6248 (mp10)
REVERT: B  323 ASP cc_start: 0.7665 (p0) cc_final: 0.7152 (p0)
REVERT: B  325 MET cc_start: 0.8553 (mmp) cc_final: 0.7471 (mtt)
REVERT: B  339 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.7098 (m100)
REVERT: D   21 MET cc_start: 0.3565 (mtm) cc_final: 0.3258 (mpp)
  outliers start: 25
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0794
  time to fit residues: 14.2447
Evaluate side-chains
  122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain D residue   59 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B 225 HIS
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.220821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.162043 restraints weight = 16510.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 4.16
r_work: 0.3274 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7407  Z= 0.154
  Angle     :  0.608  11.743  10044  Z= 0.306
  Chirality :  0.044   0.213   1134
  Planarity :  0.004   0.056   1271
  Dihedral  :  4.863  55.930   1012
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 23.59 %
    Favored  : 73.33 %
  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:  0.73 (0.28), residues: 900
  helix:  1.59 (0.25), residues: 399
  sheet: -0.03 (0.37), residues: 172
  loop : -0.53 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 197 
 TYR   0.009   0.001   TYR A 253 
 PHE   0.020   0.002   PHE B 199 
 TRP   0.022   0.001   TRP B 211 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7406)
  covalent geometry    : angle       0.60768 (10042)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       1.03665 (    2)
  hydrogen bonds       : bond        0.04332 (  413)
  hydrogen bonds       : angle       4.59120 ( 1194)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.286 
Fit side-chains
REVERT: F   29 PHE cc_start: 0.6445 (t80) cc_final: 0.6233 (t80)
REVERT: F   76 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7225 (mp)
REVERT: A   50 ASN cc_start: 0.8013 (t0) cc_final: 0.7206 (t0)
REVERT: A  209 GLU cc_start: 0.7065 (tt0) cc_final: 0.6663 (tt0)
REVERT: B  111 TYR cc_start: 0.8727 (m-80) cc_final: 0.8119 (m-80)
REVERT: B  134 ARG cc_start: 0.4997 (tpm170) cc_final: 0.4448 (tpm170)
REVERT: B  211 TRP cc_start: 0.6444 (m100) cc_final: 0.6102 (m100)
REVERT: B  212 ASP cc_start: 0.6992 (p0) cc_final: 0.6227 (p0)
REVERT: B  220 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6634 (mp10)
REVERT: B  323 ASP cc_start: 0.7736 (p0) cc_final: 0.7186 (p0)
REVERT: B  325 MET cc_start: 0.8424 (mmp) cc_final: 0.7415 (mtt)
REVERT: B  339 TRP cc_start: 0.8028 (OUTLIER) cc_final: 0.7106 (m100)
REVERT: D   21 MET cc_start: 0.3543 (mtm) cc_final: 0.3222 (mpp)
  outliers start: 24
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0792
  time to fit residues: 13.8575
Evaluate side-chains
  128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 THR
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   96 CYS
Chi-restraints excluded: chain F residue  105 MET
Chi-restraints excluded: chain F residue  126 SER
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  284 CYS
Chi-restraints excluded: chain F residue  294 ILE
Chi-restraints excluded: chain F residue  295 LEU
Chi-restraints excluded: chain F residue  319 PHE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 80 optimal weight:    0.3980
   chunk 55 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 85 optimal weight:   30.0000
   chunk 63 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.222769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.165800 restraints weight = 22816.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 4.96
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7407  Z= 0.120
  Angle     :  0.590  13.050  10044  Z= 0.293
  Chirality :  0.044   0.238   1134
  Planarity :  0.004   0.057   1271
  Dihedral  :  4.803  56.318   1012
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.10 %
    Favored  : 73.08 %
  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:  0.82 (0.28), residues: 900
  helix:  1.71 (0.25), residues: 398
  sheet:  0.04 (0.38), residues: 172
  loop : -0.55 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 197 
 TYR   0.008   0.001   TYR A 253 
 PHE   0.020   0.001   PHE B 199 
 TRP   0.022   0.001   TRP B 211 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7406)
  covalent geometry    : angle       0.58954 (10042)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.83693 (    2)
  hydrogen bonds       : bond        0.04055 (  413)
  hydrogen bonds       : angle       4.54348 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1929.25 seconds
wall clock time: 33 minutes 45.07 seconds (2025.07 seconds total)