Starting phenix.real_space_refine
on Sat Feb 15 00:00:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kal_22774/02_2025/7kal_22774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kal_22774/02_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_22774/02_2025/7kal_22774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kal_22774/02_2025/7kal_22774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kal_22774/02_2025/7kal_22774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kal_22774/02_2025/7kal_22774.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5}
          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: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 3}
          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, 'ASN:plan1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 69
  Time building chain proxies: 6.65, per 1000 atoms: 0.62
  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: 3.05
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.97
  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: 3.09

  Time building geometry restraints manager: 3.47 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:             1.300
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     26.570
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.290
-------------------------------------------------------------------------------
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= 0.142
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (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
 TRP   0.022   0.001   TRP E 141 
 HIS   0.002   0.000   HIS D 534 
 PHE   0.011   0.001   PHE D  15 
 TYR   0.013   0.001   TYR D 435 
 ARG   0.002   0.000   ARG A 238 

*********************** 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  : 1.360 
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: 0.2481
  time to fit residues: 47.0134
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  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0570
   chunk 127 optimal weight:    9.9990
   overall best weight:    3.8106

-------------------------------------------------------------------------------
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  61 GLN
D  63 GLN
D 375 GLN
D 386 GLN
D 529 GLN
D 534 HIS
D 595 GLN
D 604 HIS
** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3294 r_free = 0.3294 target = 0.055327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.044902 restraints weight = 75811.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.045963 restraints weight = 48252.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.046113 restraints weight = 29843.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11024  Z= 0.282
  Angle     :  0.599   7.206  14988  Z= 0.300
  Chirality :  0.038   0.159   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.441  18.525   1530
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.94 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.02 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1394
  helix:  1.56 (0.17), residues: 952
  sheet: -2.28 (0.52), residues: 88
  loop : -1.96 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 141 
 HIS   0.009   0.001   HIS A 336 
 PHE   0.030   0.001   PHE G 267 
 TYR   0.012   0.001   TYR D 435 
 ARG   0.008   0.000   ARG F  96 

*********************** 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
  115 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9122 (mmm) cc_final: 0.8828 (mmm)
REVERT: A  245 MET cc_start: 0.8215 (tmm) cc_final: 0.7641 (tmm)
REVERT: A  251 LEU cc_start: 0.9231 (tp) cc_final: 0.8871 (tt)
REVERT: C   54 ILE cc_start: 0.9456 (tp) cc_final: 0.9201 (tp)
REVERT: D  357 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8671 (t80)
REVERT: D  471 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8680 (pt)
REVERT: E   10 PHE cc_start: 0.8111 (m-10) cc_final: 0.7901 (m-80)
REVERT: E   84 GLU cc_start: 0.9290 (tp30) cc_final: 0.8705 (tm-30)
REVERT: E   94 GLU cc_start: 0.8349 (tp30) cc_final: 0.8016 (tp30)
REVERT: E  121 LYS cc_start: 0.9534 (ttpt) cc_final: 0.9319 (pptt)
REVERT: E  125 ASP cc_start: 0.8947 (t0) cc_final: 0.8722 (t0)
REVERT: E  152 MET cc_start: 0.8941 (mtm) cc_final: 0.8734 (mtm)
REVERT: F  100 TYR cc_start: 0.9179 (t80) cc_final: 0.8763 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1878
  time to fit residues: 30.6692
Evaluate side-chains
  101 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
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 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  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  357 PHE
Chi-restraints excluded: chain D residue  471 LEU
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 69 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 119 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 120 optimal weight:   30.0000
   chunk 13 optimal weight:    2.9990
   chunk 135 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 139 optimal weight:   30.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 336 HIS
D 622 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.055118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.045089 restraints weight = 77809.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045711 restraints weight = 42236.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.045979 restraints weight = 31071.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11024  Z= 0.241
  Angle     :  0.578   7.048  14988  Z= 0.285
  Chirality :  0.037   0.141   1752
  Planarity :  0.004   0.034   1881
  Dihedral  :  3.477  18.462   1530
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.94 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.45 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.24), residues: 1394
  helix:  1.95 (0.17), residues: 952
  sheet: -2.02 (0.55), residues: 87
  loop : -1.74 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 141 
 HIS   0.012   0.001   HIS A 336 
 PHE   0.019   0.001   PHE G 267 
 TYR   0.011   0.001   TYR D 435 
 ARG   0.007   0.000   ARG F  88 

*********************** 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
  114 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9159 (mmm) cc_final: 0.8802 (mmm)
REVERT: A  251 LEU cc_start: 0.9217 (tp) cc_final: 0.8856 (tt)
REVERT: C   54 ILE cc_start: 0.9446 (tp) cc_final: 0.9203 (tp)
REVERT: D  357 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8814 (t80)
REVERT: D  369 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9167 (tp)
REVERT: E   84 GLU cc_start: 0.9297 (tp30) cc_final: 0.8771 (tm-30)
REVERT: E   85 ASP cc_start: 0.9219 (m-30) cc_final: 0.8756 (m-30)
REVERT: E  104 GLN cc_start: 0.8926 (mp10) cc_final: 0.8678 (mp10)
REVERT: E  125 ASP cc_start: 0.8961 (t0) cc_final: 0.8757 (t0)
REVERT: E  162 MET cc_start: 0.8774 (mmm) cc_final: 0.8516 (mtp)
REVERT: F  100 TYR cc_start: 0.9207 (t80) cc_final: 0.8776 (t80)
REVERT: F  170 MET cc_start: 0.8182 (ttm) cc_final: 0.7872 (mtp)
  outliers start: 24
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1695
  time to fit residues: 29.0839
Evaluate side-chains
  102 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
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  357 PHE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  463 VAL
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 112 optimal weight:    0.9980
   chunk 116 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 134 optimal weight:   50.0000
   chunk 86 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
D  61 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.055523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.045278 restraints weight = 75593.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.046275 restraints weight = 41793.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.046656 restraints weight = 26563.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11024  Z= 0.169
  Angle     :  0.556   7.809  14988  Z= 0.270
  Chirality :  0.037   0.145   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.372  18.277   1530
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.96 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.24), residues: 1394
  helix:  2.18 (0.17), residues: 949
  sheet: -2.04 (0.54), residues: 90
  loop : -1.66 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.017   0.001   PHE G 267 
 TYR   0.010   0.001   TYR D 435 
 ARG   0.005   0.000   ARG F  88 

*********************** 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
  117 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9199 (tp) cc_final: 0.8828 (tt)
REVERT: C   54 ILE cc_start: 0.9437 (tp) cc_final: 0.9188 (tp)
REVERT: D  270 MET cc_start: 0.8457 (ppp) cc_final: 0.8228 (ppp)
REVERT: D  471 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8509 (pt)
REVERT: E   84 GLU cc_start: 0.9290 (tp30) cc_final: 0.8769 (tm-30)
REVERT: E   85 ASP cc_start: 0.9198 (m-30) cc_final: 0.8802 (m-30)
REVERT: E   94 GLU cc_start: 0.8396 (tp30) cc_final: 0.8103 (tp30)
REVERT: E  125 ASP cc_start: 0.8957 (t0) cc_final: 0.8748 (t0)
REVERT: F  100 TYR cc_start: 0.9184 (t80) cc_final: 0.8764 (t80)
REVERT: F  170 MET cc_start: 0.8349 (ttm) cc_final: 0.7997 (mtp)
  outliers start: 20
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1796
  time to fit residues: 32.5028
Evaluate side-chains
  102 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
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 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  462 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 130 optimal weight:    9.9990
   chunk 115 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9980
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.055829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.045079 restraints weight = 75568.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.045990 restraints weight = 42548.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.046744 restraints weight = 29923.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11024  Z= 0.159
  Angle     :  0.573   9.378  14988  Z= 0.274
  Chirality :  0.037   0.207   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.329  18.185   1530
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.08 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.33 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1394
  helix:  2.35 (0.17), residues: 943
  sheet: -1.91 (0.56), residues: 87
  loop : -1.52 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.017   0.001   PHE G 267 
 TYR   0.013   0.001   TYR C  53 
 ARG   0.004   0.000   ARG F  88 

*********************** 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
  120 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 2.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9200 (mmm) cc_final: 0.8837 (mmm)
REVERT: A  251 LEU cc_start: 0.9200 (tp) cc_final: 0.8828 (tt)
REVERT: A  294 MET cc_start: 0.8949 (ttp) cc_final: 0.8502 (ptm)
REVERT: C   54 ILE cc_start: 0.9439 (tp) cc_final: 0.9192 (tp)
REVERT: D   94 ILE cc_start: 0.9195 (mm) cc_final: 0.8920 (mm)
REVERT: D  369 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9066 (tp)
REVERT: E   84 GLU cc_start: 0.9309 (tp30) cc_final: 0.8791 (tm-30)
REVERT: E   85 ASP cc_start: 0.9168 (m-30) cc_final: 0.8856 (m-30)
REVERT: E  125 ASP cc_start: 0.8949 (t0) cc_final: 0.8735 (t0)
REVERT: F  100 TYR cc_start: 0.9125 (t80) cc_final: 0.8770 (t80)
REVERT: F  170 MET cc_start: 0.8274 (ttm) cc_final: 0.7707 (mtp)
  outliers start: 28
  outliers final: 15
  residues processed: 113
  average time/residue: 0.1713
  time to fit residues: 30.8815
Evaluate side-chains
  104 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
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 C residue   16 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  251 THR
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  450 ILE
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  186 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 129 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 56 optimal weight:    5.9990
   chunk 131 optimal weight:    7.9990
   chunk 114 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0980
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.7782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.055866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.045772 restraints weight = 76564.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.046626 restraints weight = 39235.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.047217 restraints weight = 27514.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11024  Z= 0.171
  Angle     :  0.582  10.301  14988  Z= 0.280
  Chirality :  0.037   0.142   1752
  Planarity :  0.004   0.040   1881
  Dihedral  :  3.329  18.235   1530
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.53 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.24), residues: 1394
  helix:  2.39 (0.17), residues: 946
  sheet: -2.08 (0.54), residues: 89
  loop : -1.40 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 225 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.001   PHE G 267 
 TYR   0.023   0.001   TYR E 158 
 ARG   0.004   0.000   ARG F  88 

*********************** 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
  124 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 1.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9241 (mmm) cc_final: 0.8756 (mmm)
REVERT: A  236 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8143 (t80)
REVERT: A  251 LEU cc_start: 0.9187 (tp) cc_final: 0.8807 (tt)
REVERT: C   54 ILE cc_start: 0.9441 (tp) cc_final: 0.9214 (tp)
REVERT: D   94 ILE cc_start: 0.9174 (mm) cc_final: 0.8896 (mm)
REVERT: D  369 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9045 (tp)
REVERT: E   84 GLU cc_start: 0.9301 (tp30) cc_final: 0.8786 (tm-30)
REVERT: E   85 ASP cc_start: 0.9131 (m-30) cc_final: 0.8842 (m-30)
REVERT: E  125 ASP cc_start: 0.8948 (t0) cc_final: 0.8725 (t0)
REVERT: F  100 TYR cc_start: 0.9196 (t80) cc_final: 0.8793 (t80)
REVERT: F  170 MET cc_start: 0.8321 (ttm) cc_final: 0.7691 (mtp)
  outliers start: 32
  outliers final: 16
  residues processed: 116
  average time/residue: 0.1759
  time to fit residues: 32.3785
Evaluate side-chains
  107 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
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  236 PHE
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
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  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  153 ASP
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 120 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.056128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.046361 restraints weight = 76835.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.046971 restraints weight = 38831.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.047131 restraints weight = 30765.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11024  Z= 0.161
  Angle     :  0.595  11.112  14988  Z= 0.283
  Chirality :  0.037   0.143   1752
  Planarity :  0.004   0.042   1881
  Dihedral  :  3.317  18.224   1530
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.94 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.39 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.24), residues: 1394
  helix:  2.43 (0.17), residues: 943
  sheet: -2.20 (0.53), residues: 90
  loop : -1.38 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.017   0.001   PHE B 106 
 TYR   0.017   0.001   TYR F 125 
 ARG   0.003   0.000   ARG F  88 

*********************** 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
  114 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9220 (mmm) cc_final: 0.8739 (mmm)
REVERT: A  236 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8187 (t80)
REVERT: A  251 LEU cc_start: 0.9192 (tp) cc_final: 0.8814 (tt)
REVERT: C   54 ILE cc_start: 0.9424 (tp) cc_final: 0.9200 (tp)
REVERT: D   94 ILE cc_start: 0.9177 (mm) cc_final: 0.8897 (mm)
REVERT: D  369 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9065 (tp)
REVERT: E   84 GLU cc_start: 0.9243 (tp30) cc_final: 0.8754 (tm-30)
REVERT: E   85 ASP cc_start: 0.9096 (m-30) cc_final: 0.8816 (m-30)
REVERT: E  162 MET cc_start: 0.8883 (mmm) cc_final: 0.8580 (tpp)
REVERT: F  100 TYR cc_start: 0.9200 (t80) cc_final: 0.8801 (t80)
REVERT: F  146 LYS cc_start: 0.9362 (tmtt) cc_final: 0.9030 (tptp)
REVERT: F  170 MET cc_start: 0.8275 (ttm) cc_final: 0.7604 (mtp)
  outliers start: 23
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1896
  time to fit residues: 32.6791
Evaluate side-chains
  105 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
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  236 PHE
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
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  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  153 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 19 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 132 optimal weight:    0.5980
   chunk 110 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
F  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.056049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045818 restraints weight = 75948.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.047029 restraints weight = 39923.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.047352 restraints weight = 24086.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11024  Z= 0.160
  Angle     :  0.584  11.337  14988  Z= 0.280
  Chirality :  0.037   0.152   1752
  Planarity :  0.004   0.045   1881
  Dihedral  :  3.308  18.346   1530
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.73 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 20.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.24), residues: 1394
  helix:  2.50 (0.17), residues: 939
  sheet: -2.26 (0.52), residues: 90
  loop : -1.32 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.013   0.001   PHE G 267 
 TYR   0.018   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

*********************** 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
  112 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9227 (mmm) cc_final: 0.8848 (mmm)
REVERT: A  251 LEU cc_start: 0.9191 (tp) cc_final: 0.8811 (tt)
REVERT: C   54 ILE cc_start: 0.9414 (tp) cc_final: 0.9180 (tp)
REVERT: D   94 ILE cc_start: 0.9148 (mm) cc_final: 0.8866 (mm)
REVERT: D  369 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8995 (tp)
REVERT: E   84 GLU cc_start: 0.9259 (tp30) cc_final: 0.8758 (tm-30)
REVERT: E   85 ASP cc_start: 0.9105 (m-30) cc_final: 0.8831 (m-30)
REVERT: F  100 TYR cc_start: 0.9208 (t80) cc_final: 0.8851 (t80)
REVERT: F  146 LYS cc_start: 0.9384 (tmtt) cc_final: 0.9154 (tptp)
REVERT: F  170 MET cc_start: 0.8230 (ttm) cc_final: 0.7546 (mtp)
  outliers start: 23
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1841
  time to fit residues: 30.6332
Evaluate side-chains
  104 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
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 C residue   16 LEU
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 139 optimal weight:   50.0000
   chunk 102 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 137 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0020
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.1996

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.056373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.046511 restraints weight = 76975.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.047142 restraints weight = 38742.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.047394 restraints weight = 31286.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11024  Z= 0.159
  Angle     :  0.610  11.917  14988  Z= 0.290
  Chirality :  0.037   0.143   1752
  Planarity :  0.004   0.046   1881
  Dihedral  :  3.307  18.208   1530
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 19.94 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.24), residues: 1394
  helix:  2.46 (0.17), residues: 944
  sheet: -2.23 (0.52), residues: 90
  loop : -1.34 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.027   0.001   PHE E  23 
 TYR   0.017   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

*********************** 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
  112 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9202 (mmm) cc_final: 0.8809 (mmm)
REVERT: A  236 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8224 (t80)
REVERT: A  251 LEU cc_start: 0.9188 (tp) cc_final: 0.8805 (tt)
REVERT: A  294 MET cc_start: 0.8921 (ttp) cc_final: 0.8444 (ptp)
REVERT: C   54 ILE cc_start: 0.9423 (tp) cc_final: 0.9196 (tp)
REVERT: D   94 ILE cc_start: 0.9151 (mm) cc_final: 0.8870 (mm)
REVERT: D  369 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9033 (tp)
REVERT: E   84 GLU cc_start: 0.9172 (tp30) cc_final: 0.8729 (tm-30)
REVERT: E   85 ASP cc_start: 0.9094 (m-30) cc_final: 0.8812 (m-30)
REVERT: F  100 TYR cc_start: 0.9188 (t80) cc_final: 0.8848 (t80)
REVERT: F  146 LYS cc_start: 0.9388 (tmtt) cc_final: 0.9146 (tptp)
REVERT: F  170 MET cc_start: 0.8223 (ttm) cc_final: 0.7718 (mtp)
  outliers start: 24
  outliers final: 15
  residues processed: 107
  average time/residue: 0.1682
  time to fit residues: 28.8285
Evaluate side-chains
  104 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
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  236 PHE
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 77 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 57 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 138 optimal weight:   20.0000
   overall best weight:    0.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.056500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.046681 restraints weight = 76148.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.047369 restraints weight = 38853.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.047614 restraints weight = 30487.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11024  Z= 0.150
  Angle     :  0.610  12.576  14988  Z= 0.289
  Chirality :  0.037   0.143   1752
  Planarity :  0.004   0.048   1881
  Dihedral  :  3.281  18.346   1530
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.51 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.59 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.24), residues: 1394
  helix:  2.49 (0.17), residues: 940
  sheet: -2.25 (0.51), residues: 90
  loop : -1.32 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.014   0.001   PHE E  23 
 TYR   0.018   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

********************** 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
  106 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9202 (mmm) cc_final: 0.8810 (mmm)
REVERT: A  236 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8289 (t80)
REVERT: A  251 LEU cc_start: 0.9182 (tp) cc_final: 0.8795 (tt)
REVERT: A  294 MET cc_start: 0.8896 (ttp) cc_final: 0.8487 (ptm)
REVERT: C   54 ILE cc_start: 0.9405 (tp) cc_final: 0.9177 (tp)
REVERT: D   94 ILE cc_start: 0.9136 (mm) cc_final: 0.8853 (mm)
REVERT: D  369 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8964 (tp)
REVERT: E   84 GLU cc_start: 0.9168 (tp30) cc_final: 0.8716 (tm-30)
REVERT: E   85 ASP cc_start: 0.9123 (m-30) cc_final: 0.8818 (m-30)
REVERT: E  162 MET cc_start: 0.8710 (mtp) cc_final: 0.8377 (mtp)
REVERT: F  100 TYR cc_start: 0.9202 (t80) cc_final: 0.8874 (t80)
REVERT: F  146 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9163 (tptp)
REVERT: F  170 MET cc_start: 0.8234 (ttm) cc_final: 0.7567 (mtp)
  outliers start: 17
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1726
  time to fit residues: 27.8081
Evaluate side-chains
  103 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
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  236 PHE
Chi-restraints excluded: chain A residue  427 CYS
Chi-restraints excluded: chain C residue   16 LEU
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 137 optimal weight:   30.0000
   chunk 77 optimal weight:    1.9990
   overall best weight:    2.7986

-------------------------------------------------------------------------------
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 = 0.3307 r_free = 0.3307 target = 0.055482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.045198 restraints weight = 76926.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.046179 restraints weight = 41687.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.046701 restraints weight = 26525.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11024  Z= 0.224
  Angle     :  0.645  11.734  14988  Z= 0.310
  Chirality :  0.038   0.141   1752
  Planarity :  0.004   0.048   1881
  Dihedral  :  3.351  19.083   1530
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.24), residues: 1394
  helix:  2.54 (0.17), residues: 943
  sheet: -2.19 (0.50), residues: 90
  loop : -1.29 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 141 
 HIS   0.002   0.001   HIS A 336 
 PHE   0.014   0.001   PHE D 563 
 TYR   0.016   0.001   TYR C  53 
 ARG   0.003   0.000   ARG E  88 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2650.87 seconds
wall clock time: 48 minutes 39.49 seconds (2919.49 seconds total)