Starting phenix.real_space_refine
on Mon Jul 28 23:40:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kal_22774/07_2025/7kal_22774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kal_22774/07_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_22774/07_2025/7kal_22774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kal_22774/07_2025/7kal_22774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kal_22774/07_2025/7kal_22774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kal_22774/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.10, per 1000 atoms: 0.57
  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: 2.80
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.93
  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: 2.75

  Time building geometry restraints manager: 3.28 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:             19.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.020
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0000

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

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.58 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 

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

*********************** 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  : 1.205 
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: 0.2364
  time to fit residues: 45.2573
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  : 1.246 
-------------------------------------------------------------------------------
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 = 75811.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.045963 restraints weight = 48251.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.046114 restraints weight = 29832.645|
|-----------------------------------------------------------------------------|
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= 0.192
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  740)
  hydrogen bonds       : angle       3.77196 ( 2199)
  covalent geometry    : bond        0.00432 (11024)
  covalent geometry    : angle       0.59888 (14988)

*********************** 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  : 1.267 
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: 0.7640 (tmm)
REVERT: A  251 LEU cc_start: 0.9232 (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: 0.8670 (t80)
REVERT: D  471 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8679 (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: 0.9318 (pptt)
REVERT: E  125 ASP cc_start: 0.8947 (t0) cc_final: 0.8723 (t0)
REVERT: E  152 MET cc_start: 0.8941 (mtm) cc_final: 0.8735 (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: 0.2131
  time to fit residues: 35.0119
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  : 1.287 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 120 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 135 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 139 optimal weight:   40.0000
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3297 r_free = 0.3297 target = 0.055217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.045224 restraints weight = 77770.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.045723 restraints weight = 42523.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.046052 restraints weight = 31831.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11024  Z= 0.160
  Angle     :  0.574   7.208  14988  Z= 0.283
  Chirality :  0.037   0.141   1752
  Planarity :  0.004   0.034   1881
  Dihedral  :  3.459  18.403   1530
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.64 %
    Favored  : 84.14 %
  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   0.013   0.001   HIS A 336 
 PHE   0.019   0.001   PHE G 267 
 TYR   0.011   0.001   TYR D 435 
 ARG   0.006   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  740)
  hydrogen bonds       : angle       3.65477 ( 2199)
  covalent geometry    : bond        0.00355 (11024)
  covalent geometry    : angle       0.57355 (14988)

*********************** 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  : 1.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.9151 (mmm) cc_final: 0.8794 (mmm)
REVERT: A  251 LEU cc_start: 0.9216 (tp) cc_final: 0.8854 (tt)
REVERT: C   54 ILE cc_start: 0.9437 (tp) cc_final: 0.9192 (tp)
REVERT: D  369 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9160 (tp)
REVERT: E   84 GLU cc_start: 0.9295 (tp30) cc_final: 0.8767 (tm-30)
REVERT: E   85 ASP cc_start: 0.9216 (m-30) cc_final: 0.8754 (m-30)
REVERT: E  104 GLN cc_start: 0.8897 (mp10) cc_final: 0.8671 (mp10)
REVERT: E  125 ASP cc_start: 0.8959 (t0) cc_final: 0.8753 (t0)
REVERT: E  162 MET cc_start: 0.8777 (mmm) cc_final: 0.8517 (mtp)
REVERT: F  100 TYR cc_start: 0.9210 (t80) cc_final: 0.8775 (t80)
REVERT: F  170 MET cc_start: 0.8178 (ttm) cc_final: 0.7859 (mtp)
  outliers start: 24
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1653
  time to fit residues: 28.6153
Evaluate side-chains
  102 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 116 optimal weight:    0.0470
   chunk 19 optimal weight:    1.9990
   chunk 134 optimal weight:   50.0000
   chunk 86 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.0084

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.055433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.045328 restraints weight = 75710.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.046180 restraints weight = 41368.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.046459 restraints weight = 27648.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
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   0.034  11024  Z= 0.126
  Angle     :  0.559   7.476  14988  Z= 0.273
  Chirality :  0.037   0.144   1752
  Planarity :  0.004   0.036   1881
  Dihedral  :  3.386  18.394   1530
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.87 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.86 %
    Favored  : 82.28 %
  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:  1.43 (0.24), residues: 1394
  helix:  2.15 (0.17), residues: 949
  sheet: -1.94 (0.55), residues: 87
  loop : -1.68 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 141 
 HIS   0.002   0.000   HIS D  56 
 PHE   0.017   0.001   PHE G 267 
 TYR   0.010   0.001   TYR D 435 
 ARG   0.005   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  740)
  hydrogen bonds       : angle       3.55414 ( 2199)
  covalent geometry    : bond        0.00280 (11024)
  covalent geometry    : angle       0.55932 (14988)

*********************** 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
  115 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9209 (tp) cc_final: 0.8839 (tt)
REVERT: C   54 ILE cc_start: 0.9444 (tp) cc_final: 0.9201 (tp)
REVERT: D  270 MET cc_start: 0.8496 (ppp) cc_final: 0.8256 (ppp)
REVERT: E   84 GLU cc_start: 0.9273 (tp30) cc_final: 0.8745 (tm-30)
REVERT: E   85 ASP cc_start: 0.9195 (m-30) cc_final: 0.8816 (m-30)
REVERT: E  125 ASP cc_start: 0.8936 (t0) cc_final: 0.8730 (t0)
REVERT: F  100 TYR cc_start: 0.9177 (t80) cc_final: 0.8758 (t80)
REVERT: F  170 MET cc_start: 0.8326 (ttm) cc_final: 0.7980 (mtp)
  outliers start: 20
  outliers final: 13
  residues processed: 109
  average time/residue: 0.2220
  time to fit residues: 38.3871
Evaluate side-chains
  102 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.940 
-------------------------------------------------------------------------------
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 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  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 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:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 130 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    4.1588

-------------------------------------------------------------------------------
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 = 0.3272 r_free = 0.3272 target = 0.054304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.044440 restraints weight = 76779.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.044624 restraints weight = 43899.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.044995 restraints weight = 34140.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11024  Z= 0.210
  Angle     :  0.643   8.788  14988  Z= 0.315
  Chirality :  0.038   0.202   1752
  Planarity :  0.004   0.038   1881
  Dihedral  :  3.551  18.845   1530
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.59 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.51 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.44 (0.24), residues: 1394
  helix:  2.17 (0.17), residues: 952
  sheet: -2.09 (0.54), residues: 90
  loop : -1.66 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 141 
 HIS   0.003   0.001   HIS F  10 
 PHE   0.018   0.002   PHE G 267 
 TYR   0.011   0.001   TYR D 435 
 ARG   0.005   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  740)
  hydrogen bonds       : angle       3.78846 ( 2199)
  covalent geometry    : bond        0.00467 (11024)
  covalent geometry    : angle       0.64307 (14988)

*********************** 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
  124 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 1.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9201 (tp) cc_final: 0.8819 (tt)
REVERT: C   54 ILE cc_start: 0.9485 (tp) cc_final: 0.9252 (tp)
REVERT: D  357 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8864 (t80)
REVERT: D  369 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9172 (tp)
REVERT: D  471 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8391 (pt)
REVERT: E   84 GLU cc_start: 0.9270 (tp30) cc_final: 0.8730 (tm-30)
REVERT: E   85 ASP cc_start: 0.9128 (m-30) cc_final: 0.8725 (m-30)
REVERT: F  100 TYR cc_start: 0.9189 (t80) cc_final: 0.8753 (t80)
REVERT: F  170 MET cc_start: 0.8423 (ttm) cc_final: 0.7904 (mtp)
  outliers start: 34
  outliers final: 21
  residues processed: 114
  average time/residue: 0.2336
  time to fit residues: 42.1068
Evaluate side-chains
  110 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
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   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
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  347 THR
Chi-restraints excluded: chain D residue  357 PHE
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  471 LEU
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue  110 ASP
Chi-restraints excluded: chain E residue  153 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 129 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 131 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0020
   chunk 46 optimal weight:    0.9990
   overall best weight:    3.3996

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.054454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.044430 restraints weight = 77002.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.044995 restraints weight = 44923.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.045184 restraints weight = 33000.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11024  Z= 0.174
  Angle     :  0.620  10.424  14988  Z= 0.302
  Chirality :  0.038   0.141   1752
  Planarity :  0.004   0.042   1881
  Dihedral  :  3.556  18.077   1530
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.16 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.00 %
    Favored  : 78.76 %
  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:  1.50 (0.24), residues: 1394
  helix:  2.21 (0.17), residues: 952
  sheet: -2.17 (0.53), residues: 90
  loop : -1.59 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 141 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.028   0.001   PHE D 563 
 TYR   0.019   0.001   TYR E 158 
 ARG   0.004   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  740)
  hydrogen bonds       : angle       3.75013 ( 2199)
  covalent geometry    : bond        0.00389 (11024)
  covalent geometry    : angle       0.61962 (14988)

*********************** 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
  123 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 88
  time to evaluate  : 2.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9205 (tp) cc_final: 0.8830 (tt)
REVERT: C   54 ILE cc_start: 0.9496 (tp) cc_final: 0.9278 (tp)
REVERT: D   94 ILE cc_start: 0.9239 (mm) cc_final: 0.8968 (mm)
REVERT: D  369 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9122 (tp)
REVERT: E   84 GLU cc_start: 0.9291 (tp30) cc_final: 0.8734 (tm-30)
REVERT: E   85 ASP cc_start: 0.9131 (m-30) cc_final: 0.8754 (m-30)
REVERT: F  100 TYR cc_start: 0.9211 (t80) cc_final: 0.8770 (t80)
REVERT: F  170 MET cc_start: 0.8469 (ttm) cc_final: 0.7825 (mtp)
  outliers start: 35
  outliers final: 21
  residues processed: 115
  average time/residue: 0.2250
  time to fit residues: 42.5061
Evaluate side-chains
  110 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 1.973 
-------------------------------------------------------------------------------
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   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  251 THR
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  353 ILE
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue  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:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 103 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 120 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 = 0.3289 r_free = 0.3289 target = 0.054823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.045032 restraints weight = 77403.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.045347 restraints weight = 44647.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.045695 restraints weight = 33240.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2305

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= 0.141
  Angle     :  0.605  10.595  14988  Z= 0.292
  Chirality :  0.037   0.153   1752
  Planarity :  0.004   0.044   1881
  Dihedral  :  3.493  17.501   1530
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.23 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.39 %
    Favored  : 78.29 %
  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:  1.65 (0.24), residues: 1394
  helix:  2.31 (0.17), residues: 946
  sheet: -2.19 (0.52), residues: 90
  loop : -1.44 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 141 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.022   0.001   PHE D 563 
 TYR   0.014   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03754 (  740)
  hydrogen bonds       : angle       3.65250 ( 2199)
  covalent geometry    : bond        0.00313 (11024)
  covalent geometry    : angle       0.60529 (14988)

*********************** 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
  113 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9194 (tp) cc_final: 0.8817 (tt)
REVERT: C   54 ILE cc_start: 0.9479 (tp) cc_final: 0.9248 (tp)
REVERT: D   94 ILE cc_start: 0.9235 (mm) cc_final: 0.8934 (mm)
REVERT: D  369 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9144 (tp)
REVERT: E   84 GLU cc_start: 0.9269 (tp30) cc_final: 0.8708 (tm-30)
REVERT: E   85 ASP cc_start: 0.9149 (m-30) cc_final: 0.8848 (m-30)
REVERT: E  162 MET cc_start: 0.8922 (mmm) cc_final: 0.8440 (mtp)
REVERT: F  100 TYR cc_start: 0.9188 (t80) cc_final: 0.8776 (t80)
REVERT: F  125 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8637 (m-10)
REVERT: F  146 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9102 (tptp)
REVERT: F  170 MET cc_start: 0.8386 (ttm) cc_final: 0.7738 (mtp)
  outliers start: 25
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1623
  time to fit residues: 28.0051
Evaluate side-chains
  109 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
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 C residue   57 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue   19 CYS
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  125 TYR
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 6 optimal weight:    0.2980
   chunk 19 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.055391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.045250 restraints weight = 76650.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.046140 restraints weight = 42176.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.046383 restraints weight = 28260.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11024  Z= 0.115
  Angle     :  0.614  11.206  14988  Z= 0.290
  Chirality :  0.037   0.143   1752
  Planarity :  0.004   0.047   1881
  Dihedral  :  3.410  17.050   1530
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 19.48 %
    Favored  : 78.01 %
  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:  2.38 (0.17), residues: 946
  sheet: -2.19 (0.51), residues: 90
  loop : -1.33 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 141 
 HIS   0.003   0.000   HIS A 336 
 PHE   0.019   0.001   PHE C  45 
 TYR   0.013   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  740)
  hydrogen bonds       : angle       3.52325 ( 2199)
  covalent geometry    : bond        0.00251 (11024)
  covalent geometry    : angle       0.61369 (14988)

*********************** 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
  120 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.8817 (tpp) cc_final: 0.8589 (ttt)
REVERT: A  251 LEU cc_start: 0.9181 (tp) cc_final: 0.8799 (tt)
REVERT: C   54 ILE cc_start: 0.9454 (tp) cc_final: 0.9242 (tp)
REVERT: D   94 ILE cc_start: 0.9204 (mm) cc_final: 0.8905 (mm)
REVERT: D  369 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9060 (tp)
REVERT: E   84 GLU cc_start: 0.9192 (tp30) cc_final: 0.8722 (tm-30)
REVERT: E   85 ASP cc_start: 0.9151 (m-30) cc_final: 0.8864 (m-30)
REVERT: E  162 MET cc_start: 0.8882 (mmm) cc_final: 0.8430 (mtp)
REVERT: F  100 TYR cc_start: 0.9201 (t80) cc_final: 0.8798 (t80)
REVERT: F  125 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8580 (m-10)
REVERT: F  146 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9153 (tptp)
REVERT: F  170 MET cc_start: 0.8331 (ttm) cc_final: 0.7642 (mtp)
  outliers start: 27
  outliers final: 17
  residues processed: 112
  average time/residue: 0.2077
  time to fit residues: 36.4952
Evaluate side-chains
  111 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
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 C residue   57 LEU
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
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  153 ASP
Chi-restraints excluded: chain F residue  125 TYR
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 139 optimal weight:   40.0000
   chunk 102 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 137 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.3313 r_free = 0.3313 target = 0.055600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.045464 restraints weight = 77326.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.046462 restraints weight = 43175.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.046706 restraints weight = 28157.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2406

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= 0.119
  Angle     :  0.616  11.743  14988  Z= 0.295
  Chirality :  0.037   0.159   1752
  Planarity :  0.004   0.048   1881
  Dihedral  :  3.393  16.466   1530
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.39 %
    Favored  : 78.20 %
  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:  1.79 (0.24), residues: 1394
  helix:  2.41 (0.17), residues: 945
  sheet: -2.19 (0.51), residues: 90
  loop : -1.28 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 141 
 HIS   0.003   0.001   HIS A 133 
 PHE   0.019   0.001   PHE C  45 
 TYR   0.018   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  740)
  hydrogen bonds       : angle       3.51568 ( 2199)
  covalent geometry    : bond        0.00262 (11024)
  covalent geometry    : angle       0.61582 (14988)

*********************** 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
  118 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9175 (tp) cc_final: 0.8798 (tt)
REVERT: A  294 MET cc_start: 0.8900 (ttp) cc_final: 0.8503 (ptm)
REVERT: C   54 ILE cc_start: 0.9445 (tp) cc_final: 0.9223 (tp)
REVERT: D   94 ILE cc_start: 0.9176 (mm) cc_final: 0.8885 (mm)
REVERT: D  369 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9068 (tp)
REVERT: E   84 GLU cc_start: 0.9177 (tp30) cc_final: 0.8661 (tm-30)
REVERT: E   85 ASP cc_start: 0.9125 (m-30) cc_final: 0.8841 (m-30)
REVERT: E  162 MET cc_start: 0.8866 (mmm) cc_final: 0.8410 (mtp)
REVERT: F  100 TYR cc_start: 0.9181 (t80) cc_final: 0.8789 (t80)
REVERT: F  125 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8555 (m-10)
REVERT: F  146 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9146 (tptp)
REVERT: F  170 MET cc_start: 0.8324 (ttm) cc_final: 0.7690 (mtp)
  outliers start: 26
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1626
  time to fit residues: 28.6525
Evaluate side-chains
  109 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
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 C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain E residue  153 ASP
Chi-restraints excluded: chain F residue  125 TYR
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 77 optimal weight:    0.2980
   chunk 80 optimal weight:    3.9990
   chunk 128 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 57 optimal weight:   20.0000
   chunk 73 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0030
   chunk 83 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 138 optimal weight:   30.0000
   overall best weight:    2.0594

-------------------------------------------------------------------------------
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 = 0.3301 r_free = 0.3301 target = 0.055175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.045027 restraints weight = 77019.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.046076 restraints weight = 42042.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.046164 restraints weight = 27139.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11024  Z= 0.132
  Angle     :  0.639  12.018  14988  Z= 0.305
  Chirality :  0.038   0.151   1752
  Planarity :  0.004   0.051   1881
  Dihedral  :  3.412  15.937   1530
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.50 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.79 (0.24), residues: 1394
  helix:  2.39 (0.17), residues: 946
  sheet: -2.15 (0.50), residues: 90
  loop : -1.25 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 225 
 HIS   0.002   0.000   HIS A 336 
 PHE   0.016   0.001   PHE B 106 
 TYR   0.018   0.001   TYR C  53 
 ARG   0.003   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  740)
  hydrogen bonds       : angle       3.54576 ( 2199)
  covalent geometry    : bond        0.00295 (11024)
  covalent geometry    : angle       0.63943 (14988)

********************** 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
  109 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9185 (tp) cc_final: 0.8805 (tt)
REVERT: A  294 MET cc_start: 0.8899 (ttp) cc_final: 0.8467 (ptm)
REVERT: C   54 ILE cc_start: 0.9470 (tp) cc_final: 0.9255 (tp)
REVERT: D   94 ILE cc_start: 0.9168 (mm) cc_final: 0.8876 (mm)
REVERT: D  369 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9082 (tp)
REVERT: E   84 GLU cc_start: 0.9219 (tp30) cc_final: 0.8673 (tm-30)
REVERT: E   85 ASP cc_start: 0.9180 (m-30) cc_final: 0.8885 (m-30)
REVERT: E  162 MET cc_start: 0.8894 (mmm) cc_final: 0.8443 (mtp)
REVERT: F  100 TYR cc_start: 0.9193 (t80) cc_final: 0.8787 (t80)
REVERT: F  125 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8588 (m-10)
REVERT: F  146 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9182 (tptp)
REVERT: F  170 MET cc_start: 0.8366 (ttm) cc_final: 0.7703 (mtp)
  outliers start: 19
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1994
  time to fit residues: 32.0316
Evaluate side-chains
  108 residues out of total 1193 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
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 C residue   66 LEU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain D residue  206 LEU
Chi-restraints excluded: chain D residue  211 SER
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  369 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  450 ILE
Chi-restraints excluded: chain D residue  462 VAL
Chi-restraints excluded: chain D residue  463 VAL
Chi-restraints excluded: chain D residue  603 LEU
Chi-restraints excluded: chain F residue  125 TYR
Chi-restraints excluded: chain F residue  146 LYS
Chi-restraints excluded: chain F residue  186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 137 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.054803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.044738 restraints weight = 76913.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.045506 restraints weight = 41874.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.045819 restraints weight = 28825.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11024  Z= 0.163
  Angle     :  0.666  11.909  14988  Z= 0.321
  Chirality :  0.038   0.141   1752
  Planarity :  0.004   0.051   1881
  Dihedral  :  3.463  15.717   1530
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.52 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.78 %
    Favored  : 77.37 %
  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:  2.37 (0.17), residues: 946
  sheet: -2.09 (0.51), residues: 90
  loop : -1.26 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 141 
 HIS   0.002   0.001   HIS F  10 
 PHE   0.018   0.001   PHE B 106 
 TYR   0.016   0.001   TYR C  53 
 ARG   0.003   0.000   ARG D 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  740)
  hydrogen bonds       : angle       3.65332 ( 2199)
  covalent geometry    : bond        0.00364 (11024)
  covalent geometry    : angle       0.66590 (14988)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3164.74 seconds
wall clock time: 58 minutes 36.29 seconds (3516.29 seconds total)