Starting phenix.real_space_refine
on Sat Aug 23 08:18:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kal_22774/08_2025/7kal_22774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kal_22774/08_2025/7kal_22774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kal_22774/08_2025/7kal_22774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kal_22774/08_2025/7kal_22774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kal_22774/08_2025/7kal_22774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kal_22774/08_2025/7kal_22774.cif"
  }
  resolution = 4.0
  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=   0.005 sd=   0.057
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    7021      2.51       5
     N    1853      2.21       5
     O    1868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10789
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3264
          Classifications: {'peptide': 437}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 21, 'TRANS': 415}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 7, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "C"
      Number of atoms: 440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 440
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 245
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 3673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3673
          Classifications: {'peptide': 475}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 31, 'TRANS': 443}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "E"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1359
          Classifications: {'peptide': 172}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "F"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1454
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 15, 'TRANS': 178}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "G"
      Number of atoms: 354
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 354
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 145
          Unresolved non-hydrogen angles: 188
          Unresolved non-hydrogen dihedrals: 126
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 69
  Time building chain proxies: 2.67, per 1000 atoms: 0.25
  Number of scatterers: 10789
  At special positions: 0
  Unit cell: (109.44, 126.54, 137.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1868      8.00
     N    1853      7.00
     C    7021      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 425.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2662

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 7 sheets defined
      69.2% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 48
      removed outlier: 3.557A  pdb=" N   LEU A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 99
    Processing helix  chain 'A' and resid 107 through 137
      removed outlier: 3.509A  pdb=" N   ARG A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLY A 137 " --> pdb=" O   HIS A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 149 through 173
      removed outlier: 3.644A  pdb=" N   LEU A 153 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLU A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 198
    Processing helix  chain 'A' and resid 213 through 225
      removed outlier: 3.540A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TRP A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.584A  pdb=" N   LEU A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLY A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 312
      removed outlier: 3.601A  pdb=" N   MET A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 324
    Processing helix  chain 'A' and resid 340 through 346
    Processing helix  chain 'A' and resid 350 through 356
    Processing helix  chain 'A' and resid 357 through 383
      removed outlier: 4.330A  pdb=" N   GLU A 381 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A 382 " --> pdb=" O   THR A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 398
    Processing helix  chain 'A' and resid 408 through 439
      removed outlier: 3.778A  pdb=" N   GLU A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      Proline residue:  A 418  - end of helix
      removed outlier: 3.682A  pdb=" N   ALA A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 464
      removed outlier: 3.503A  pdb=" N   ILE A 447 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 26
    Processing helix  chain 'C' and resid 30 through 68
      removed outlier: 3.569A  pdb=" N   PHE C  34 " --> pdb=" O   ASP C  30 " (cutoff:3.500A)
      Proline residue:  C  61  - end of helix
    Processing helix  chain 'B' and resid 95 through 123
      removed outlier: 3.551A  pdb=" N   PHE B 123 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 28
    Processing helix  chain 'D' and resid 30 through 35
      removed outlier: 4.117A  pdb=" N   LEU D  34 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 68
      removed outlier: 3.964A  pdb=" N   LEU D  68 " --> pdb=" O   LYS D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 98
      removed outlier: 4.335A  pdb=" N   ILE D  78 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   ALA D  79 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 231
      removed outlier: 4.776A  pdb=" N   LYS D 203 " --> pdb=" O   GLU D 199 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   TYR D 204 " --> pdb=" O   GLY D 200 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU D 217 " --> pdb=" O   LEU D 213 " (cutoff:3.500A)
      Proline residue:  D 218  - end of helix
      removed outlier: 4.217A  pdb=" N   TYR D 231 " --> pdb=" O   GLY D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 247
      removed outlier: 3.671A  pdb=" N   ARG D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLU D 247 " --> pdb=" O   ASN D 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 262
      removed outlier: 3.745A  pdb=" N   VAL D 258 " --> pdb=" O   GLY D 254 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASN D 259 " --> pdb=" O   GLY D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 271
      removed outlier: 3.884A  pdb=" N   GLU D 269 " --> pdb=" O   GLU D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 291
      removed outlier: 3.573A  pdb=" N   GLY D 279 " --> pdb=" O   LYS D 275 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   ALA D 281 " --> pdb=" O   GLU D 277 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   LYS D 282 " --> pdb=" O   GLU D 278 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP D 291 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 306
      removed outlier: 4.084A  pdb=" N   VAL D 302 " --> pdb=" O   LYS D 298 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE D 306 " --> pdb=" O   VAL D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 322
    Processing helix  chain 'D' and resid 331 through 358
      removed outlier: 4.186A  pdb=" N   GLU D 335 " --> pdb=" O   VAL D 331 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER D 341 " --> pdb=" O   TYR D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 360 through 376
      removed outlier: 3.668A  pdb=" N   ARG D 368 " --> pdb=" O   ILE D 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 399
      removed outlier: 3.848A  pdb=" N   SER D 397 " --> pdb=" O   LYS D 393 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU D 399 " --> pdb=" O   VAL D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 414
    Processing helix  chain 'D' and resid 419 through 424
    Processing helix  chain 'D' and resid 431 through 443
    Processing helix  chain 'E' and resid 4 through 37
      Proline residue:  E   9  - end of helix
    Processing helix  chain 'E' and resid 46 through 61
    Processing helix  chain 'E' and resid 70 through 106
      removed outlier: 3.968A  pdb=" N   LEU E  74 " --> pdb=" O   PRO E  70 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLN E  97 " --> pdb=" O   ARG E  93 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   GLN E 104 " --> pdb=" O   ALA E 100 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ARG E 105 " --> pdb=" O   LEU E 101 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY E 106 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 138
      removed outlier: 3.907A  pdb=" N   TRP E 113 " --> pdb=" O   GLY E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.926A  pdb=" N   GLN E 147 " --> pdb=" O   GLN E 143 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR E 168 " --> pdb=" O   GLU E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 168 through 180
      removed outlier: 3.836A  pdb=" N   GLU E 172 " --> pdb=" O   THR E 168 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 56
      removed outlier: 3.823A  pdb=" N   ASP F  56 " --> pdb=" O   LEU F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 68 through 89
      removed outlier: 4.426A  pdb=" N   SER F  72 " --> pdb=" O   ASN F  68 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY F  89 " --> pdb=" O   ALA F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 107
    Processing helix  chain 'F' and resid 114 through 135
    Processing helix  chain 'F' and resid 137 through 152
    Processing helix  chain 'F' and resid 156 through 171
    Processing helix  chain 'F' and resid 172 through 187
    Processing helix  chain 'F' and resid 192 through 203
    Processing helix  chain 'G' and resid 245 through 266
      removed outlier: 3.681A  pdb=" N   LEU G 266 " --> pdb=" O   PHE G 262 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 267 through 270
    Processing helix  chain 'G' and resid 274 through 305
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20
      removed outlier: 7.022A  pdb=" N   GLU A  19 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'D' and resid 448 through 457
      removed outlier: 5.564A  pdb=" N   ILE D 450 " --> pdb=" O   ARG D 476 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ARG D 476 " --> pdb=" O   ILE D 450 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LYS D 452 " --> pdb=" O   LYS D 474 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 560
      removed outlier: 3.623A  pdb=" N   VAL D 560 " --> pdb=" O   LEU D 550 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LEU D 550 " --> pdb=" O   VAL D 560 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 15

    740 hydrogen bonds defined for protein.
    2199 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: 1.73

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3430
        1.34 -     1.46: 2212
        1.46 -     1.58: 5301
        1.58 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 11024
  Sorted by residual:
  bond pdb=" N   GLY G 245 "
       pdb=" CA  GLY G 245 "
    ideal  model  delta    sigma   weight residual
    1.443  1.459 -0.017 1.37e-02 5.33e+03 1.46e+00
  bond pdb=" CA  VAL G 283 "
       pdb=" CB  VAL G 283 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.012 1.25e-02 6.40e+03 9.43e-01
  bond pdb=" C   PRO F  57 "
       pdb=" N   PRO F  58 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.42e-01
  bond pdb=" N   PRO G 246 "
       pdb=" CA  PRO G 246 "
    ideal  model  delta    sigma   weight residual
    1.472  1.459  0.013 1.32e-02 5.74e+03 9.18e-01
  bond pdb=" CA  ILE G 297 "
       pdb=" CB  ILE G 297 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.012 1.25e-02 6.40e+03 8.61e-01
  ... (remaining 11019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 14612
        1.36 -     2.72: 294
        2.72 -     4.09: 56
        4.09 -     5.45: 18
        5.45 -     6.81: 8
  Bond angle restraints: 14988
  Sorted by residual:
  angle pdb=" N   PRO G 246 "
        pdb=" CA  PRO G 246 "
        pdb=" CB  PRO G 246 "
      ideal   model   delta    sigma   weight residual
     103.33  110.14   -6.81 1.10e+00 8.26e-01 3.83e+01
  angle pdb=" C   ILE A 417 "
        pdb=" CA  ILE A 417 "
        pdb=" CB  ILE A 417 "
      ideal   model   delta    sigma   weight residual
     114.00  110.71    3.29 1.31e+00 5.83e-01 6.30e+00
  angle pdb=" N   ALA D 535 "
        pdb=" CA  ALA D 535 "
        pdb=" CB  ALA D 535 "
      ideal   model   delta    sigma   weight residual
     111.66  109.08    2.58 1.11e+00 8.12e-01 5.41e+00
  angle pdb=" C   VAL A 416 "
        pdb=" N   ILE A 417 "
        pdb=" CA  ILE A 417 "
      ideal   model   delta    sigma   weight residual
     120.33  122.17   -1.84 8.00e-01 1.56e+00 5.27e+00
  angle pdb=" C   ALA D 535 "
        pdb=" CA  ALA D 535 "
        pdb=" CB  ALA D 535 "
      ideal   model   delta    sigma   weight residual
     111.20  109.64    1.56 7.10e-01 1.98e+00 4.82e+00
  ... (remaining 14983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 6123
       17.76 -    35.52: 386
       35.52 -    53.28: 53
       53.28 -    71.04: 12
       71.04 -    88.80: 6
  Dihedral angle restraints: 6580
    sinusoidal: 2457
      harmonic: 4123
  Sorted by residual:
  dihedral pdb=" CA  GLY D 426 "
           pdb=" C   GLY D 426 "
           pdb=" N   PRO D 427 "
           pdb=" CA  PRO D 427 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.73   19.27     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  LEU D 327 "
           pdb=" C   LEU D 327 "
           pdb=" N   GLU D 328 "
           pdb=" CA  GLU D 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.22  -18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLU D 328 "
           pdb=" C   GLU D 328 "
           pdb=" N   ASP D 329 "
           pdb=" CA  ASP D 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.18   16.82     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 6577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1414
       0.045 -    0.089: 286
       0.089 -    0.134: 48
       0.134 -    0.178: 3
       0.178 -    0.223: 1
  Chirality restraints: 1752
  Sorted by residual:
  chirality pdb=" CA  PRO G 246 "
            pdb=" N   PRO G 246 "
            pdb=" C   PRO G 246 "
            pdb=" CB  PRO G 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  ILE D 473 "
            pdb=" CA  ILE D 473 "
            pdb=" CG1 ILE D 473 "
            pdb=" CG2 ILE D 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.72e-01
  chirality pdb=" CA  THR A  14 "
            pdb=" N   THR A  14 "
            pdb=" C   THR A  14 "
            pdb=" CB  THR A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 1749 not shown)

  Planarity restraints: 1881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE G 267 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO G 268 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO G 268 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G 268 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO F  57 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO F  58 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO F  58 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F  58 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F  56 "   -0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO F  57 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO F  57 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F  57 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1878 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2512
        2.79 -     3.32: 10874
        3.32 -     3.84: 17415
        3.84 -     4.37: 17492
        4.37 -     4.90: 31120
  Nonbonded interactions: 79413
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D  63 "
            pdb=" OE2 GLU D 334 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   THR D 464 "
            pdb=" OG  SER D 467 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NE2 GLN D 371 "
            pdb=" O   TYR D 610 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OG1 THR D 232 "
            pdb=" O   GLY E 106 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OD1 ASN A 243 "
            pdb=" ND2 ASN A 246 "
     model   vdw
     2.300 3.120
  ... (remaining 79408 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.370
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11024  Z= 0.113
  Angle     :  0.511   6.810  14988  Z= 0.283
  Chirality :  0.036   0.223   1752
  Planarity :  0.003   0.033   1881
  Dihedral  : 11.874  88.798   3918
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.58 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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 aren not related in a simple way.
  whole: -0.72 (0.22), residues: 1394
  helix:  0.50 (0.16), residues: 940
  sheet: -2.56 (0.52), residues: 88
  loop : -2.39 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.013   0.001   TYR D 435 
 PHE   0.011   0.001   PHE D  15 
 TRP   0.022   0.001   TRP E 141 
 HIS   0.002   0.000   HIS D 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (11024)
  covalent geometry    : angle       0.51100 (14988)
  hydrogen bonds       : bond        0.10928 (  740)
  hydrogen bonds       : angle       4.22447 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9145 (tp) cc_final: 0.8805 (tt)
REVERT: C   54 ILE cc_start: 0.9296 (tp) cc_final: 0.9049 (tp)
REVERT: E   10 PHE cc_start: 0.7975 (m-10) cc_final: 0.7745 (m-80)
REVERT: E   84 GLU cc_start: 0.9140 (tp30) cc_final: 0.8729 (tm-30)
REVERT: E  104 GLN cc_start: 0.8546 (mp10) cc_final: 0.8191 (mp10)
REVERT: E  121 LYS cc_start: 0.9453 (ttpt) cc_final: 0.9220 (pptt)
REVERT: E  125 ASP cc_start: 0.8761 (t0) cc_final: 0.8530 (t0)
REVERT: F  100 TYR cc_start: 0.9348 (t80) cc_final: 0.9008 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1154
  time to fit residues: 22.0864
Evaluate side-chains
  92 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 133 HIS
A 246 ASN
A 336 HIS
D  63 GLN
D 375 GLN
D 386 GLN
D 529 GLN
D 534 HIS
D 595 GLN
D 604 HIS
D 622 GLN
E  95 GLN
E  97 GLN
F  10 HIS
F  49 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.055844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.045487 restraints weight = 75790.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.046604 restraints weight = 46670.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.046762 restraints weight = 28658.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.046899 restraints weight = 26928.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.046958 restraints weight = 25013.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11024  Z= 0.150
  Angle     :  0.573   7.442  14988  Z= 0.285
  Chirality :  0.037   0.164   1752
  Planarity :  0.004   0.033   1881
  Dihedral  :  3.380  18.186   1530
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.73 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.02 %
    Favored  : 88.50 %
  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 aren not related in a simple way.
  whole:  0.70 (0.23), residues: 1394
  helix:  1.58 (0.17), residues: 952
  sheet: -2.27 (0.53), residues: 88
  loop : -1.91 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  96 
 TYR   0.012   0.001   TYR D 435 
 PHE   0.028   0.001   PHE G 267 
 TRP   0.012   0.001   TRP E 141 
 HIS   0.009   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (11024)
  covalent geometry    : angle       0.57317 (14988)
  hydrogen bonds       : bond        0.03724 (  740)
  hydrogen bonds       : angle       3.66520 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9117 (mmm) cc_final: 0.8797 (mmm)
REVERT: A  245 MET cc_start: 0.8166 (tmm) cc_final: 0.7606 (tmm)
REVERT: A  251 LEU cc_start: 0.9214 (tp) cc_final: 0.8856 (tt)
REVERT: A  345 MET cc_start: 0.9103 (tpp) cc_final: 0.8867 (tpp)
REVERT: C   54 ILE cc_start: 0.9434 (tp) cc_final: 0.9180 (tp)
REVERT: E   84 GLU cc_start: 0.9277 (tp30) cc_final: 0.8690 (tm-30)
REVERT: E  121 LYS cc_start: 0.9502 (ttpt) cc_final: 0.9281 (pptt)
REVERT: E  125 ASP cc_start: 0.8918 (t0) cc_final: 0.8682 (t0)
REVERT: E  152 MET cc_start: 0.8920 (mtm) cc_final: 0.8719 (mtm)
REVERT: F  100 TYR cc_start: 0.9159 (t80) cc_final: 0.8744 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0836
  time to fit residues: 13.4310
Evaluate side-chains
  102 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 HIS
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0770
   chunk 123 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.3944

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

Flipped N/Q/H residues before XYZ refinement:
A 336 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.055918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.046115 restraints weight = 76630.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.046457 restraints weight = 45941.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.046943 restraints weight = 32446.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.046982 restraints weight = 27307.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.047038 restraints weight = 25509.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11024  Z= 0.138
  Angle     :  0.559   7.548  14988  Z= 0.274
  Chirality :  0.037   0.142   1752
  Planarity :  0.004   0.034   1881
  Dihedral  :  3.367  18.188   1530
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.52 %
    Favored  : 85.44 %
  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 aren not related in a simple way.
  whole:  1.26 (0.24), residues: 1394
  helix:  2.01 (0.17), residues: 949
  sheet: -2.00 (0.54), residues: 88
  loop : -1.69 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  96 
 TYR   0.022   0.001   TYR E 158 
 PHE   0.019   0.001   PHE G 267 
 TRP   0.012   0.001   TRP E 141 
 HIS   0.014   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11024)
  covalent geometry    : angle       0.55864 (14988)
  hydrogen bonds       : bond        0.03614 (  740)
  hydrogen bonds       : angle       3.56476 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9159 (mmm) cc_final: 0.8838 (mmm)
REVERT: A  245 MET cc_start: 0.8138 (tmm) cc_final: 0.7565 (tmm)
REVERT: A  251 LEU cc_start: 0.9215 (tp) cc_final: 0.8852 (tt)
REVERT: C   54 ILE cc_start: 0.9420 (tp) cc_final: 0.9164 (tp)
REVERT: D  207 MET cc_start: 0.6964 (mmt) cc_final: 0.6671 (mmp)
REVERT: D  471 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8521 (pt)
REVERT: E   84 GLU cc_start: 0.9256 (tp30) cc_final: 0.8739 (tm-30)
REVERT: E   85 ASP cc_start: 0.9179 (m-30) cc_final: 0.8789 (m-30)
REVERT: E  104 GLN cc_start: 0.8866 (mp10) cc_final: 0.8663 (mp10)
REVERT: E  121 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9291 (pptt)
REVERT: E  125 ASP cc_start: 0.8942 (t0) cc_final: 0.8725 (t0)
REVERT: F  100 TYR cc_start: 0.9211 (t80) cc_final: 0.8777 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0885
  time to fit residues: 15.0625
Evaluate side-chains
  105 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  471 LEU
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 117 optimal weight:   20.0000
   chunk 60 optimal weight:    8.9990
   chunk 135 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 138 optimal weight:   30.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  61 GLN
D 542 HIS
D 584 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.053373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.043358 restraints weight = 78483.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.043852 restraints weight = 44633.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.043990 restraints weight = 35266.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.044154 restraints weight = 30569.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.044230 restraints weight = 27772.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  11024  Z= 0.302
  Angle     :  0.719   7.509  14988  Z= 0.360
  Chirality :  0.040   0.139   1752
  Planarity :  0.004   0.034   1881
  Dihedral  :  3.767  19.143   1530
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.45 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.14 %
    Favored  : 80.71 %
  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 aren not related in a simple way.
  whole:  1.04 (0.24), residues: 1394
  helix:  1.83 (0.17), residues: 958
  sheet: -2.10 (0.54), residues: 88
  loop : -1.82 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 587 
 TYR   0.029   0.002   TYR E 158 
 PHE   0.034   0.002   PHE E  10 
 TRP   0.021   0.002   TRP E 141 
 HIS   0.004   0.001   HIS F  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 (11024)
  covalent geometry    : angle       0.71892 (14988)
  hydrogen bonds       : bond        0.04429 (  740)
  hydrogen bonds       : angle       4.10387 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 MET cc_start: 0.9092 (tpp) cc_final: 0.8879 (tpp)
REVERT: A  460 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9166 (ptp)
REVERT: C   54 ILE cc_start: 0.9492 (tp) cc_final: 0.9274 (tp)
REVERT: D  369 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9244 (tp)
REVERT: E   84 GLU cc_start: 0.9281 (tp30) cc_final: 0.8750 (tm-30)
REVERT: E   85 ASP cc_start: 0.9111 (m-30) cc_final: 0.8636 (m-30)
REVERT: E  104 GLN cc_start: 0.9086 (mp10) cc_final: 0.8876 (mp10)
REVERT: F  100 TYR cc_start: 0.9176 (t80) cc_final: 0.8755 (t80)
  outliers start: 34
  outliers final: 21
  residues processed: 113
  average time/residue: 0.0833
  time to fit residues: 14.7633
Evaluate side-chains
  109 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  153 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 133 optimal weight:   30.0000
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.054826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.044849 restraints weight = 76851.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.045398 restraints weight = 41449.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045601 restraints weight = 31585.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.045742 restraints weight = 28030.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.045833 restraints weight = 25659.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11024  Z= 0.130
  Angle     :  0.592   8.659  14988  Z= 0.291
  Chirality :  0.037   0.145   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.543  17.283   1530
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.08 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.44 %
    Favored  : 79.96 %
  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 aren not related in a simple way.
  whole:  1.40 (0.24), residues: 1394
  helix:  2.13 (0.17), residues: 952
  sheet: -2.11 (0.54), residues: 88
  loop : -1.66 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  88 
 TYR   0.013   0.001   TYR E 158 
 PHE   0.049   0.001   PHE E  10 
 TRP   0.020   0.001   TRP E 141 
 HIS   0.003   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11024)
  covalent geometry    : angle       0.59216 (14988)
  hydrogen bonds       : bond        0.03918 (  740)
  hydrogen bonds       : angle       3.71356 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9191 (mmm) cc_final: 0.8690 (mmm)
REVERT: A  251 LEU cc_start: 0.9210 (tp) cc_final: 0.8841 (tt)
REVERT: A  345 MET cc_start: 0.9126 (tpp) cc_final: 0.8843 (tpp)
REVERT: A  460 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9102 (ptp)
REVERT: C   54 ILE cc_start: 0.9475 (tp) cc_final: 0.9239 (tp)
REVERT: D  369 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9121 (tp)
REVERT: E   84 GLU cc_start: 0.9279 (tp30) cc_final: 0.8726 (tm-30)
REVERT: E   85 ASP cc_start: 0.9151 (m-30) cc_final: 0.8712 (m-30)
REVERT: F  100 TYR cc_start: 0.9178 (t80) cc_final: 0.8749 (t80)
REVERT: F  146 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9188 (tptp)
  outliers start: 28
  outliers final: 18
  residues processed: 115
  average time/residue: 0.0805
  time to fit residues: 14.6878
Evaluate side-chains
  110 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 102 optimal weight:    0.0570
   chunk 19 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 130 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    2.8106

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

Flipped N/Q/H residues before XYZ refinement:
D  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.054646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044732 restraints weight = 77716.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.045232 restraints weight = 42870.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.045454 restraints weight = 33015.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045551 restraints weight = 29075.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.045646 restraints weight = 26701.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11024  Z= 0.154
  Angle     :  0.607   8.987  14988  Z= 0.295
  Chirality :  0.037   0.164   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.541  17.071   1530
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.59 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.81 %
    Favored  : 79.13 %
  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 aren not related in a simple way.
  whole:  1.53 (0.24), residues: 1394
  helix:  2.23 (0.17), residues: 952
  sheet: -2.12 (0.53), residues: 88
  loop : -1.60 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  88 
 TYR   0.041   0.001   TYR E 158 
 PHE   0.044   0.001   PHE E  10 
 TRP   0.017   0.001   TRP E 141 
 HIS   0.003   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (11024)
  covalent geometry    : angle       0.60736 (14988)
  hydrogen bonds       : bond        0.03836 (  740)
  hydrogen bonds       : angle       3.72720 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9201 (mmm) cc_final: 0.8710 (mmm)
REVERT: A  251 LEU cc_start: 0.9198 (tp) cc_final: 0.8821 (tt)
REVERT: A  291 MET cc_start: 0.9364 (tpp) cc_final: 0.9147 (tpp)
REVERT: A  294 MET cc_start: 0.8942 (ttp) cc_final: 0.8539 (ptm)
REVERT: A  460 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.9128 (ptp)
REVERT: C   54 ILE cc_start: 0.9477 (tp) cc_final: 0.9241 (tp)
REVERT: D   94 ILE cc_start: 0.9245 (mm) cc_final: 0.8969 (mm)
REVERT: D  369 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9185 (tp)
REVERT: E   84 GLU cc_start: 0.9262 (tp30) cc_final: 0.8707 (tm-30)
REVERT: E   85 ASP cc_start: 0.9096 (m-30) cc_final: 0.8740 (m-30)
REVERT: F  100 TYR cc_start: 0.9153 (t80) cc_final: 0.8746 (t80)
REVERT: F  146 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9038 (tptp)
  outliers start: 33
  outliers final: 17
  residues processed: 120
  average time/residue: 0.0828
  time to fit residues: 15.5910
Evaluate side-chains
  108 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  146 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 9 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 99 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.054589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.044778 restraints weight = 77001.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.045076 restraints weight = 43385.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.045438 restraints weight = 32936.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.045560 restraints weight = 27711.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.045634 restraints weight = 25887.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11024  Z= 0.153
  Angle     :  0.627  10.358  14988  Z= 0.300
  Chirality :  0.037   0.143   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.526  16.635   1530
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.37 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.20 %
    Favored  : 78.11 %
  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 aren not related in a simple way.
  whole:  1.59 (0.24), residues: 1394
  helix:  2.28 (0.17), residues: 952
  sheet: -2.28 (0.52), residues: 90
  loop : -1.54 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  88 
 TYR   0.035   0.001   TYR E 158 
 PHE   0.043   0.001   PHE E  10 
 TRP   0.015   0.001   TRP E 141 
 HIS   0.003   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11024)
  covalent geometry    : angle       0.62678 (14988)
  hydrogen bonds       : bond        0.03797 (  740)
  hydrogen bonds       : angle       3.69780 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9193 (mmm) cc_final: 0.8755 (mmm)
REVERT: A  251 LEU cc_start: 0.9199 (tp) cc_final: 0.8822 (tt)
REVERT: A  294 MET cc_start: 0.8987 (ttp) cc_final: 0.8403 (ptp)
REVERT: A  460 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9150 (ptp)
REVERT: C   54 ILE cc_start: 0.9484 (tp) cc_final: 0.9263 (tp)
REVERT: D   94 ILE cc_start: 0.9239 (mm) cc_final: 0.8936 (mm)
REVERT: D  369 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9139 (tp)
REVERT: E   84 GLU cc_start: 0.9281 (tp30) cc_final: 0.8712 (tm-30)
REVERT: E   85 ASP cc_start: 0.9129 (m-30) cc_final: 0.8787 (m-30)
REVERT: F  100 TYR cc_start: 0.9173 (t80) cc_final: 0.8769 (t80)
REVERT: F  146 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9143 (tptp)
  outliers start: 29
  outliers final: 22
  residues processed: 110
  average time/residue: 0.0789
  time to fit residues: 13.9822
Evaluate side-chains
  111 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  373 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 124 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 82 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0670
   chunk 16 optimal weight:    9.9990
   chunk 118 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    2.6126

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** 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 = 0.3284 r_free = 0.3284 target = 0.054614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.044654 restraints weight = 77424.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.045108 restraints weight = 45210.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.045418 restraints weight = 33175.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.045506 restraints weight = 29224.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.045598 restraints weight = 27137.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11024  Z= 0.147
  Angle     :  0.619   9.764  14988  Z= 0.298
  Chirality :  0.037   0.142   1752
  Planarity :  0.004   0.042   1881
  Dihedral  :  3.522  16.657   1530
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.52 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.20 %
    Favored  : 77.92 %
  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 aren not related in a simple way.
  whole:  1.63 (0.24), residues: 1394
  helix:  2.31 (0.17), residues: 952
  sheet: -2.30 (0.51), residues: 90
  loop : -1.50 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  88 
 TYR   0.037   0.001   TYR E 158 
 PHE   0.035   0.001   PHE E  10 
 TRP   0.013   0.001   TRP E 141 
 HIS   0.002   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11024)
  covalent geometry    : angle       0.61919 (14988)
  hydrogen bonds       : bond        0.03769 (  740)
  hydrogen bonds       : angle       3.62581 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9201 (mmm) cc_final: 0.8978 (mmm)
REVERT: A  251 LEU cc_start: 0.9196 (tp) cc_final: 0.8818 (tt)
REVERT: A  294 MET cc_start: 0.8978 (ttp) cc_final: 0.8502 (ptm)
REVERT: A  460 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9159 (ptp)
REVERT: C   54 ILE cc_start: 0.9473 (tp) cc_final: 0.9249 (tp)
REVERT: D   94 ILE cc_start: 0.9233 (mm) cc_final: 0.8928 (mm)
REVERT: D  369 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9142 (tp)
REVERT: E   84 GLU cc_start: 0.9207 (tp30) cc_final: 0.8689 (tm-30)
REVERT: E   85 ASP cc_start: 0.9193 (m-30) cc_final: 0.8841 (m-30)
REVERT: F  100 TYR cc_start: 0.9186 (t80) cc_final: 0.8779 (t80)
REVERT: F  146 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9115 (tptp)
  outliers start: 31
  outliers final: 19
  residues processed: 110
  average time/residue: 0.0825
  time to fit residues: 14.5992
Evaluate side-chains
  110 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 95 optimal weight:    0.3980
   chunk 16 optimal weight:    9.9990
   chunk 92 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** 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 = 0.3279 r_free = 0.3279 target = 0.054354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.044588 restraints weight = 77225.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.045127 restraints weight = 42944.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.045418 restraints weight = 32042.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.045512 restraints weight = 26506.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.045592 restraints weight = 24894.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11024  Z= 0.169
  Angle     :  0.648   9.808  14988  Z= 0.311
  Chirality :  0.038   0.141   1752
  Planarity :  0.004   0.041   1881
  Dihedral  :  3.583  17.980   1530
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.66 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.57 %
    Favored  : 77.74 %
  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 aren not related in a simple way.
  whole:  1.62 (0.24), residues: 1394
  helix:  2.30 (0.17), residues: 952
  sheet: -2.27 (0.50), residues: 90
  loop : -1.48 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  88 
 TYR   0.045   0.001   TYR E 158 
 PHE   0.036   0.001   PHE E  10 
 TRP   0.016   0.001   TRP E 176 
 HIS   0.002   0.001   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11024)
  covalent geometry    : angle       0.64820 (14988)
  hydrogen bonds       : bond        0.03847 (  740)
  hydrogen bonds       : angle       3.67596 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9175 (mmm) cc_final: 0.8935 (mmm)
REVERT: A  251 LEU cc_start: 0.9196 (tp) cc_final: 0.8821 (tt)
REVERT: A  294 MET cc_start: 0.8951 (ttp) cc_final: 0.8506 (ptm)
REVERT: A  460 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9106 (ptp)
REVERT: C   54 ILE cc_start: 0.9483 (tp) cc_final: 0.9247 (tp)
REVERT: D   94 ILE cc_start: 0.9228 (mm) cc_final: 0.8922 (mm)
REVERT: D  369 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9099 (tp)
REVERT: E   84 GLU cc_start: 0.9194 (tp30) cc_final: 0.8692 (tm-30)
REVERT: E   85 ASP cc_start: 0.9107 (m-30) cc_final: 0.8769 (m-30)
REVERT: E  121 LYS cc_start: 0.9438 (ttpt) cc_final: 0.9196 (pptt)
REVERT: F  100 TYR cc_start: 0.9148 (t80) cc_final: 0.8762 (t80)
REVERT: F  146 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9132 (tptp)
  outliers start: 29
  outliers final: 22
  residues processed: 108
  average time/residue: 0.0803
  time to fit residues: 13.9236
Evaluate side-chains
  112 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  373 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 138 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 136 optimal weight:    4.9990
   chunk 15 optimal weight:   20.0000
   chunk 127 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0670
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0270
   overall best weight:    2.0182

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** 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 = 0.3291 r_free = 0.3291 target = 0.054809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.044854 restraints weight = 76604.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.045570 restraints weight = 41713.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.045884 restraints weight = 29070.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.045988 restraints weight = 25680.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.046109 restraints weight = 23780.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11024  Z= 0.132
  Angle     :  0.634  11.050  14988  Z= 0.303
  Chirality :  0.038   0.147   1752
  Planarity :  0.004   0.043   1881
  Dihedral  :  3.522  16.003   1530
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.30 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.13 %
    Favored  : 77.64 %
  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 aren not related in a simple way.
  whole:  1.74 (0.24), residues: 1394
  helix:  2.37 (0.17), residues: 946
  sheet: -2.17 (0.51), residues: 90
  loop : -1.36 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  88 
 TYR   0.049   0.001   TYR E 158 
 PHE   0.036   0.001   PHE E  10 
 TRP   0.014   0.001   TRP E 141 
 HIS   0.002   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (11024)
  covalent geometry    : angle       0.63429 (14988)
  hydrogen bonds       : bond        0.03729 (  740)
  hydrogen bonds       : angle       3.54914 ( 2199)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.8840 (tpp) cc_final: 0.8578 (ttt)
REVERT: A   78 MET cc_start: 0.9162 (mmm) cc_final: 0.8925 (mmm)
REVERT: A  251 LEU cc_start: 0.9183 (tp) cc_final: 0.8799 (tt)
REVERT: A  294 MET cc_start: 0.8918 (ttp) cc_final: 0.8481 (ptm)
REVERT: A  460 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9120 (ptp)
REVERT: C   54 ILE cc_start: 0.9471 (tp) cc_final: 0.9249 (tp)
REVERT: D   94 ILE cc_start: 0.9202 (mm) cc_final: 0.8897 (mm)
REVERT: D  369 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9090 (tp)
REVERT: E   84 GLU cc_start: 0.9190 (tp30) cc_final: 0.8657 (tm-30)
REVERT: E   85 ASP cc_start: 0.9156 (m-30) cc_final: 0.8836 (m-30)
REVERT: F  100 TYR cc_start: 0.9165 (t80) cc_final: 0.8789 (t80)
REVERT: F  146 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9148 (tptp)
  outliers start: 24
  outliers final: 19
  residues processed: 107
  average time/residue: 0.0840
  time to fit residues: 14.1656
Evaluate side-chains
  108 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 66 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0370
   chunk 22 optimal weight:    0.2980
   chunk 125 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.4664

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** 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 = 0.3285 r_free = 0.3285 target = 0.054629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.044863 restraints weight = 77381.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.045249 restraints weight = 42730.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.045603 restraints weight = 32287.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.045687 restraints weight = 27170.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.045801 restraints weight = 25525.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11024  Z= 0.145
  Angle     :  0.644  11.736  14988  Z= 0.309
  Chirality :  0.038   0.142   1752
  Planarity :  0.004   0.041   1881
  Dihedral  :  3.527  17.446   1530
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.44 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.22 %
    Favored  : 77.46 %
  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 aren not related in a simple way.
  whole:  1.73 (0.24), residues: 1394
  helix:  2.35 (0.17), residues: 946
  sheet: -2.12 (0.51), residues: 90
  loop : -1.32 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  88 
 TYR   0.058   0.001   TYR E 158 
 PHE   0.036   0.001   PHE E  10 
 TRP   0.015   0.001   TRP E 141 
 HIS   0.002   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11024)
  covalent geometry    : angle       0.64401 (14988)
  hydrogen bonds       : bond        0.03776 (  740)
  hydrogen bonds       : angle       3.58174 ( 2199)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1590.42 seconds
wall clock time: 28 minutes 26.08 seconds (1706.08 seconds total)