Starting phenix.real_space_refine
on Sun Jan 19 07:20:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx0_37896/01_2025/8wx0_37896.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx0_37896/01_2025/8wx0_37896.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx0_37896/01_2025/8wx0_37896.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx0_37896/01_2025/8wx0_37896.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx0_37896/01_2025/8wx0_37896.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx0_37896/01_2025/8wx0_37896.cif"
  }
  resolution = 3.7
  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=   0.002 sd=   0.145
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: 5
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     S      49      5.16       5
     C    8536      2.51       5
     N    2338      2.21       5
     O    2738      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13672
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4478
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 29, 'TRANS': 567}
    Chain: "B"
      Number of atoms: 4447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4447
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 29, 'TRANS': 562}
    Chain: "C"
      Number of atoms: 4452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4452
          Classifications: {'peptide': 593}
          Link IDs: {'PTRANS': 29, 'TRANS': 563}
    Chain: "E"
      Number of atoms: 122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 122
          Classifications: {'RNA': 6}
          Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 2, 'rna3p': 3}
    Chain: "F"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Classifications: {'RNA': 3}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 1}
    Chain: "G"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Classifications: {'RNA': 3}
          Modifications used: {'5*END': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 2}
    Chain: "D"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 59
          Classifications: {'RNA': 3}
          Modifications used: {'rna3p_pyr': 3}
          Link IDs: {'rna3p': 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 8.51, per 1000 atoms: 0.62
  Number of scatterers: 13672
  At special positions: 0
  Unit cell: (110.88, 103.84, 123.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P      11     15.00
     O    2738      8.00
     N    2338      7.00
     C    8536      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.31
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3246

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 10 sheets defined
      36.9% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 78 through 83
    Processing helix  chain 'A' and resid 97 through 115
      Proline residue:  A 110  - end of helix
      Proline residue:  A 113  - end of helix
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 178 through 185
    Processing helix  chain 'A' and resid 212 through 219
    Processing helix  chain 'A' and resid 225 through 236
    Processing helix  chain 'A' and resid 236 through 249
      removed outlier: 3.873A  pdb=" N   GLN A 247 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 282
    Processing helix  chain 'A' and resid 283 through 289
    Processing helix  chain 'A' and resid 294 through 314
      removed outlier: 3.855A  pdb=" N   GLU A 304 " --> pdb=" O   GLN A 300 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   VAL A 310 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN A 311 " --> pdb=" O   THR A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 344
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 414 through 418
      removed outlier: 3.828A  pdb=" N   THR A 418 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 443
    Processing helix  chain 'A' and resid 444 through 446
      No H-bonds generated for 'chain 'A' and resid 444 through 446'
    Processing helix  chain 'A' and resid 469 through 485
    Processing helix  chain 'A' and resid 527 through 532
      removed outlier: 3.725A  pdb=" N   PHE A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 584
    Processing helix  chain 'B' and resid 78 through 83
    Processing helix  chain 'B' and resid 98 through 112
      removed outlier: 3.974A  pdb=" N   CYS B 104 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 138 through 154
      removed outlier: 3.844A  pdb=" N   GLY B 154 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 184
      removed outlier: 3.693A  pdb=" N   ARG B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 225 through 234
    Processing helix  chain 'B' and resid 236 through 246
    Processing helix  chain 'B' and resid 253 through 258
      removed outlier: 4.065A  pdb=" N   SER B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 281
      removed outlier: 3.556A  pdb=" N   TYR B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   VAL B 281 " --> pdb=" O   SER B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.638A  pdb=" N   LEU B 286 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ALA B 287 " --> pdb=" O   ASP B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 314
      removed outlier: 3.924A  pdb=" N   ILE B 302 " --> pdb=" O   ARG B 298 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU B 304 " --> pdb=" O   GLN B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 343
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 414 through 418
      removed outlier: 3.507A  pdb=" N   THR B 418 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 443
    Processing helix  chain 'B' and resid 444 through 446
      No H-bonds generated for 'chain 'B' and resid 444 through 446'
    Processing helix  chain 'B' and resid 469 through 485
    Processing helix  chain 'B' and resid 558 through 584
      removed outlier: 4.146A  pdb=" N   ALA B 583 " --> pdb=" O   VAL B 579 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 23
      removed outlier: 3.658A  pdb=" N   GLY C  23 " --> pdb=" O   GLY C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 83
    Processing helix  chain 'C' and resid 97 through 112
      Proline residue:  C 110  - end of helix
    Processing helix  chain 'C' and resid 138 through 153
    Processing helix  chain 'C' and resid 178 through 183
      removed outlier: 3.675A  pdb=" N   GLU C 183 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 218
    Processing helix  chain 'C' and resid 225 through 236
    Processing helix  chain 'C' and resid 236 through 249
    Processing helix  chain 'C' and resid 273 through 282
      removed outlier: 3.523A  pdb=" N   SER C 277 " --> pdb=" O   ASP C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 291
    Processing helix  chain 'C' and resid 297 through 314
      removed outlier: 3.836A  pdb=" N   ARG C 301 " --> pdb=" O   GLU C 297 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU C 304 " --> pdb=" O   GLN C 300 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 342
    Processing helix  chain 'C' and resid 389 through 393
    Processing helix  chain 'C' and resid 414 through 418
      removed outlier: 3.690A  pdb=" N   THR C 418 " --> pdb=" O   PRO C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 443
    Processing helix  chain 'C' and resid 444 through 446
      No H-bonds generated for 'chain 'C' and resid 444 through 446'
    Processing helix  chain 'C' and resid 469 through 485
    Processing helix  chain 'C' and resid 525 through 532
    Processing helix  chain 'C' and resid 558 through 584
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175
      removed outlier: 4.095A  pdb=" N   PHE A 187 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ASP A 188 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ALA A 207 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   VAL A 190 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   VAL A 205 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ALA A 192 " --> pdb=" O   MET A 203 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   MET A 203 " --> pdb=" O   THR A 552 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   VAL A 545 " --> pdb=" O   THR A 541 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   THR A 541 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A 535 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE A 536 " --> pdb=" O   MET A 497 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 521 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 362
      removed outlier: 6.777A  pdb=" N   LEU A 382 " --> pdb=" O   ALA A 462 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   ALA A 462 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL A 384 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
      removed outlier: 5.249A  pdb=" N   SER A 460 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   THR A 386 " --> pdb=" O   GLN A 458 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   GLN A 458 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ASP A 388 " --> pdb=" O   ILE A 456 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   ILE A 456 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 18
    Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 175
      removed outlier: 6.781A  pdb=" N   ASP B 188 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA B 207 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL B 190 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL B 205 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ALA B 192 " --> pdb=" O   MET B 203 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   MET B 203 " --> pdb=" O   THR B 552 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASP B 551 " --> pdb=" O   ASP B 535 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASP B 535 " --> pdb=" O   ASP B 551 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 358 through 362
      removed outlier: 6.200A  pdb=" N   GLN B 380 " --> pdb=" O   LEU B 463 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   MET B 408 " --> pdb=" O   GLN B 458 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   SER B 460 " --> pdb=" O   MET B 408 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   HIS B 410 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   ALA B 462 " --> pdb=" O   HIS B 410 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   ASN B 412 " --> pdb=" O   ALA B 462 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   GLY B 464 " --> pdb=" O   ASN B 412 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 17
      removed outlier: 6.554A  pdb=" N   MET C  51 " --> pdb=" O   LEU C 130 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   THR C  72 " --> pdb=" O   ILE C 125 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   VAL C 127 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ASP C  74 " --> pdb=" O   VAL C 127 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   ILE C 129 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   GLU C  76 " --> pdb=" O   ILE C 129 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   SER C 131 " --> pdb=" O   GLU C  76 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 175
      removed outlier: 4.197A  pdb=" N   PHE C 187 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ASP C 188 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ALA C 207 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL C 190 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   VAL C 205 " --> pdb=" O   VAL C 190 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ALA C 192 " --> pdb=" O   MET C 203 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   THR C 546 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 358 through 362
      removed outlier: 6.338A  pdb=" N   GLN C 380 " --> pdb=" O   LEU C 463 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP C 388 " --> pdb=" O   ALA C 455 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   MET C 408 " --> pdb=" O   GLN C 458 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   SER C 460 " --> pdb=" O   MET C 408 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   HIS C 410 " --> pdb=" O   SER C 460 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   ALA C 462 " --> pdb=" O   HIS C 410 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   ASN C 412 " --> pdb=" O   ALA C 462 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   GLY C 464 " --> pdb=" O   ASN C 412 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 499 through 506
      removed outlier: 3.677A  pdb=" N   VAL C 513 " --> pdb=" O   VAL C 506 " (cutoff:3.500A)

    676 hydrogen bonds defined for protein.
    1881 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: 4.36

  Time building geometry restraints manager: 3.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4641
        1.34 -     1.46: 2024
        1.46 -     1.58: 7135
        1.58 -     1.70: 22
        1.70 -     1.82: 89
  Bond restraints: 13911
  Sorted by residual:
  bond pdb=" N   PHE B  11 "
       pdb=" CA  PHE B  11 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.72e+00
  bond pdb=" N   VAL B  10 "
       pdb=" CA  VAL B  10 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.37e-02 5.33e+03 6.31e+00
  bond pdb=" N   GLY C 498 "
       pdb=" CA  GLY C 498 "
    ideal  model  delta    sigma   weight residual
    1.449  1.475 -0.026 1.08e-02 8.57e+03 5.78e+00
  bond pdb=" N   MET C 497 "
       pdb=" CA  MET C 497 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.46e+00
  bond pdb=" N   GLU C  77 "
       pdb=" CA  GLU C  77 "
    ideal  model  delta    sigma   weight residual
    1.463  1.490 -0.027 1.30e-02 5.92e+03 4.22e+00
  ... (remaining 13906 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 18435
        1.54 -     3.09: 408
        3.09 -     4.63: 75
        4.63 -     6.17: 23
        6.17 -     7.71: 4
  Bond angle restraints: 18945
  Sorted by residual:
  angle pdb=" CA  GLY C 498 "
        pdb=" C   GLY C 498 "
        pdb=" O   GLY C 498 "
      ideal   model   delta    sigma   weight residual
     122.39  118.18    4.21 1.25e+00 6.40e-01 1.14e+01
  angle pdb=" CA  GLU C  77 "
        pdb=" C   GLU C  77 "
        pdb=" O   GLU C  77 "
      ideal   model   delta    sigma   weight residual
     122.41  118.44    3.97 1.21e+00 6.83e-01 1.07e+01
  angle pdb=" N   THR B 316 "
        pdb=" CA  THR B 316 "
        pdb=" C   THR B 316 "
      ideal   model   delta    sigma   weight residual
     114.56  110.91    3.65 1.27e+00 6.20e-01 8.25e+00
  angle pdb=" C   VAL C 510 "
        pdb=" N   ASP C 511 "
        pdb=" CA  ASP C 511 "
      ideal   model   delta    sigma   weight residual
     121.54  126.96   -5.42 1.91e+00 2.74e-01 8.05e+00
  angle pdb=" CA  ALA C 496 "
        pdb=" C   ALA C 496 "
        pdb=" O   ALA C 496 "
      ideal   model   delta    sigma   weight residual
     121.39  118.27    3.12 1.12e+00 7.97e-01 7.77e+00
  ... (remaining 18940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.83: 8061
       34.83 -    69.67: 370
       69.67 -   104.50: 26
      104.50 -   139.34: 0
      139.34 -   174.17: 2
  Dihedral angle restraints: 8459
    sinusoidal: 3401
      harmonic: 5058
  Sorted by residual:
  dihedral pdb=" O4'   U D   2 "
           pdb=" C1'   U D   2 "
           pdb=" N1    U D   2 "
           pdb=" C2    U D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -11.10 -148.90     1      1.50e+01 4.44e-03 7.92e+01
  dihedral pdb=" O4'   U E   6 "
           pdb=" C1'   U E   6 "
           pdb=" N1    U E   6 "
           pdb=" C2    U E   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   57.83  174.17     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" C3'   U D   1 "
           pdb=" C4'   U D   1 "
           pdb=" O4'   U D   1 "
           pdb=" C1'   U D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00   -4.89   24.89     1      8.00e+00 1.56e-02 1.39e+01
  ... (remaining 8456 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 2068
       0.089 -    0.178: 164
       0.178 -    0.267: 3
       0.267 -    0.356: 1
       0.356 -    0.446: 1
  Chirality restraints: 2237
  Sorted by residual:
  chirality pdb=" P     U D   2 "
            pdb=" OP1   U D   2 "
            pdb=" OP2   U D   2 "
            pdb=" O5'   U D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.86   -0.45 2.00e-01 2.50e+01 4.96e+00
  chirality pdb=" CB  ILE A   6 "
            pdb=" CA  ILE A   6 "
            pdb=" CG1 ILE A   6 "
            pdb=" CG2 ILE A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" C3'   U D   2 "
            pdb=" C4'   U D   2 "
            pdb=" O3'   U D   2 "
            pdb=" C2'   U D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.71    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 2234 not shown)

  Planarity restraints: 2462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  61 "   -0.062 5.00e-02 4.00e+02   9.43e-02 1.42e+01
        pdb=" N   PRO B  62 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO B  62 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B  62 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 173 "   -0.014 2.00e-02 2.50e+03   1.38e-02 4.78e+00
        pdb=" CG  TRP B 173 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 173 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 173 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 173 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 173 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 173 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 173 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 173 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 173 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 490 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO C 491 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 491 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 491 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 2459 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1431
        2.75 -     3.28: 13737
        3.28 -     3.82: 22578
        3.82 -     4.36: 25675
        4.36 -     4.90: 45458
  Nonbonded interactions: 108879
  Sorted by model distance:
  nonbonded pdb=" O   SER C 470 "
            pdb=" OG  SER C 473 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR A 411 "
            pdb=" OG1 THR A 469 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" N   GLU A 226 "
            pdb=" OE1 GLU A 226 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   HIS B 344 "
            pdb=" ND1 HIS B 344 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   LEU A 111 "
            pdb=" OG  SER A 114 "
     model   vdw
     2.235 3.040
  ... (remaining 108874 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 6 through 596)
  selection = (chain 'B' and resid 6 through 596)
  selection = (chain 'C' and resid 6 through 596)
}
ncs_group {
  reference = (chain 'D' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ 
me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or  \ 
name O2 or name N3 or name C4 or name O4 or name C5 or name C6 )) or resid 2 thr \ 
ough 3))
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     31.930
  Find NCS groups from input model:        0.860
  Set up NCS constraints:                  0.060
  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:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
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      :  0.003   0.036  13911  Z= 0.199
  Angle     :  0.583   7.714  18945  Z= 0.306
  Chirality :  0.045   0.446   2237
  Planarity :  0.004   0.094   2462
  Dihedral  : 18.728 174.171   5213
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.50 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 35.72 %
    Favored  : 63.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.35 (0.21), residues: 1776
  helix:  1.68 (0.22), residues: 551
  sheet: -0.04 (0.24), residues: 426
  loop : -0.58 (0.24), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP B 173 
 HIS   0.001   0.001   HIS A 409 
 PHE   0.015   0.001   PHE C 531 
 TYR   0.012   0.001   TYR B  80 
 ARG   0.008   0.000   ARG C 517 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 185
  time to evaluate  : 1.551 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 3
  residues processed: 189
  average time/residue: 0.2489
  time to fit residues: 70.2460
Evaluate side-chains
  178 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 175
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  466 ASN
Chi-restraints excluded: chain B residue  189 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 149 optimal weight:   10.0000
   chunk 134 optimal weight:    8.9990
   chunk 74 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 138 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 160 optimal weight:    8.9990
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 466 ASN
B  61 ASN
B 308 GLN
C 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.145892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.115843 restraints weight = 17677.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.116759 restraints weight = 13505.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.117476 restraints weight = 11838.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       41 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.0680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  13911  Z= 0.356
  Angle     :  0.611   6.523  18945  Z= 0.313
  Chirality :  0.046   0.273   2237
  Planarity :  0.005   0.062   2462
  Dihedral  : 10.462 173.770   2146
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.24 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 32.24 %
    Favored  : 61.65 %
  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:  0.21 (0.21), residues: 1776
  helix:  1.34 (0.22), residues: 565
  sheet: -0.07 (0.24), residues: 435
  loop : -0.55 (0.25), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 173 
 HIS   0.003   0.001   HIS A 409 
 PHE   0.015   0.002   PHE A 416 
 TYR   0.017   0.002   TYR C 411 
 ARG   0.006   0.001   ARG A 329 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 179
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  329 ARG cc_start: 0.7466 (ptp90) cc_final: 0.7228 (ptp-110)
REVERT: A  420 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7079 (mp0)
REVERT: A  574 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8393 (mm)
REVERT: B  312 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6143 (ttp80)
REVERT: C   53 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9204 (tp)
REVERT: C  202 ILE cc_start: 0.8594 (mm) cc_final: 0.8259 (mm)
REVERT: C  379 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8228 (m)
  outliers start: 86
  outliers final: 50
  residues processed: 244
  average time/residue: 0.2369
  time to fit residues: 86.3308
Evaluate side-chains
  218 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 163
  time to evaluate  : 1.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  541 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 150 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 155 optimal weight:    0.5980
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B  61 ASN
B 549 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.155626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.126322 restraints weight = 17041.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.128724 restraints weight = 12217.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.130016 restraints weight = 9879.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13911  Z= 0.175
  Angle     :  0.530   7.065  18945  Z= 0.270
  Chirality :  0.044   0.267   2237
  Planarity :  0.004   0.046   2462
  Dihedral  : 10.158 174.969   2141
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.22 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 33.10 %
    Favored  : 61.65 %
  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:  0.36 (0.21), residues: 1776
  helix:  1.57 (0.22), residues: 563
  sheet:  0.05 (0.24), residues: 430
  loop : -0.58 (0.25), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 173 
 HIS   0.002   0.000   HIS B 344 
 PHE   0.013   0.001   PHE B 416 
 TYR   0.011   0.001   TYR C  80 
 ARG   0.005   0.000   ARG A  84 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 192
  time to evaluate  : 1.432 
Fit side-chains
   revert: symmetry clash
REVERT: A  329 ARG cc_start: 0.7392 (ptp90) cc_final: 0.7138 (ptp-110)
REVERT: A  420 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7033 (mp0)
REVERT: B  473 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8522 (p)
REVERT: C  202 ILE cc_start: 0.8440 (mm) cc_final: 0.8001 (mm)
REVERT: C  534 MET cc_start: 0.7103 (tmm) cc_final: 0.6862 (tmm)
  outliers start: 74
  outliers final: 43
  residues processed: 243
  average time/residue: 0.2320
  time to fit residues: 84.6358
Evaluate side-chains
  216 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 168 optimal weight:    5.9990
   chunk 125 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 127 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 154 optimal weight:   10.0000
   chunk 176 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  61 ASN
** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.144121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.113735 restraints weight = 17806.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.114529 restraints weight = 14102.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.115935 restraints weight = 11970.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.097  13911  Z= 0.439
  Angle     :  0.651   7.867  18945  Z= 0.333
  Chirality :  0.047   0.273   2237
  Planarity :  0.005   0.050   2462
  Dihedral  : 10.322 173.546   2141
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.74 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  8.31 %
    Allowed  : 29.97 %
    Favored  : 61.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.13 (0.21), residues: 1776
  helix:  1.25 (0.22), residues: 564
  sheet: -0.10 (0.24), residues: 435
  loop : -0.60 (0.25), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP B 173 
 HIS   0.004   0.001   HIS A 409 
 PHE   0.017   0.002   PHE A 416 
 TYR   0.022   0.002   TYR C 411 
 ARG   0.008   0.000   ARG A  84 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 117
    poor density    : 176
  time to evaluate  : 1.499 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7133 (mp0)
REVERT: A  574 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8496 (mm)
REVERT: B  292 ILE cc_start: 0.3680 (OUTLIER) cc_final: 0.3443 (mp)
REVERT: B  355 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6827 (mp)
REVERT: B  387 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8278 (mt)
REVERT: C    8 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5433 (mp0)
REVERT: C   53 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9210 (tp)
REVERT: C   78 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7795 (mmt-90)
REVERT: C  202 ILE cc_start: 0.8523 (mm) cc_final: 0.8291 (mm)
REVERT: C  344 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.5895 (t70)
  outliers start: 117
  outliers final: 76
  residues processed: 268
  average time/residue: 0.2514
  time to fit residues: 101.9265
Evaluate side-chains
  250 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 166
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 ASN
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 ILE
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  557 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  541 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 151 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 131 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 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 = 0.3596 r_free = 0.3596 target = 0.145447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.115124 restraints weight = 17794.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.115591 restraints weight = 14518.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.117297 restraints weight = 12240.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  13911  Z= 0.333
  Angle     :  0.614  12.243  18945  Z= 0.311
  Chirality :  0.046   0.362   2237
  Planarity :  0.004   0.049   2462
  Dihedral  : 10.247 173.589   2141
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.07 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  8.03 %
    Allowed  : 29.83 %
    Favored  : 62.14 %
  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:  0.10 (0.21), residues: 1776
  helix:  1.28 (0.22), residues: 564
  sheet: -0.16 (0.24), residues: 435
  loop : -0.62 (0.25), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 173 
 HIS   0.003   0.001   HIS B 344 
 PHE   0.018   0.002   PHE B 416 
 TYR   0.016   0.002   TYR C 411 
 ARG   0.007   0.000   ARG A  84 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 113
    poor density    : 182
  time to evaluate  : 1.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7205 (mmm160)
REVERT: A  420 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7123 (mp0)
REVERT: A  574 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (mm)
REVERT: B  222 GLN cc_start: 0.7818 (pp30) cc_final: 0.7211 (pt0)
REVERT: B  292 ILE cc_start: 0.3628 (OUTLIER) cc_final: 0.3415 (mp)
REVERT: B  312 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6340 (ttp80)
REVERT: B  387 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8312 (mt)
REVERT: C    8 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5426 (mp0)
REVERT: C   53 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9200 (tp)
REVERT: C  202 ILE cc_start: 0.8446 (mm) cc_final: 0.8201 (mm)
REVERT: C  344 HIS cc_start: 0.6797 (OUTLIER) cc_final: 0.5884 (t70)
REVERT: C  534 MET cc_start: 0.7373 (tmm) cc_final: 0.7085 (tmm)
REVERT: C  550 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (tt)
  outliers start: 113
  outliers final: 84
  residues processed: 270
  average time/residue: 0.2466
  time to fit residues: 98.7826
Evaluate side-chains
  265 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 172
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 ASN
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  264 PHE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  292 ILE
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  284 ASP
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  541 THR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  577 LEU
Chi-restraints excluded: chain C residue  584 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 171 optimal weight:    4.9990
   chunk 129 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 89 optimal weight:    0.8980
   chunk 132 optimal weight:    8.9990
   chunk 114 optimal weight:   20.0000
   chunk 120 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 505 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 = 0.3589 r_free = 0.3589 target = 0.144921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.115360 restraints weight = 17827.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.115610 restraints weight = 13823.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.116321 restraints weight = 11862.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  13911  Z= 0.347
  Angle     :  0.623  12.505  18945  Z= 0.315
  Chirality :  0.046   0.317   2237
  Planarity :  0.004   0.049   2462
  Dihedral  : 10.220 174.016   2141
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.52 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  8.45 %
    Allowed  : 30.18 %
    Favored  : 61.36 %
  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:  0.08 (0.21), residues: 1776
  helix:  1.27 (0.22), residues: 564
  sheet: -0.20 (0.24), residues: 435
  loop : -0.63 (0.25), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B 173 
 HIS   0.003   0.001   HIS A 409 
 PHE   0.019   0.002   PHE C 531 
 TYR   0.017   0.002   TYR C 411 
 ARG   0.007   0.000   ARG A  84 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 119
    poor density    : 185
  time to evaluate  : 1.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 ARG cc_start: 0.7566 (mmm160) cc_final: 0.7247 (mmm160)
REVERT: A  420 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7125 (mp0)
REVERT: A  574 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8540 (mm)
REVERT: B   11 PHE cc_start: 0.4978 (m-80) cc_final: 0.4730 (m-80)
REVERT: B  222 GLN cc_start: 0.7848 (pp30) cc_final: 0.7242 (pt0)
REVERT: B  276 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5974 (m-80)
REVERT: B  312 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6342 (ttp80)
REVERT: B  355 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7036 (mp)
REVERT: C    8 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5442 (mp0)
REVERT: C   53 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9214 (tp)
REVERT: C  202 ILE cc_start: 0.8417 (mm) cc_final: 0.8156 (mm)
REVERT: C  344 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.5891 (t70)
REVERT: C  534 MET cc_start: 0.7389 (tmm) cc_final: 0.7064 (tmm)
REVERT: C  550 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8069 (tt)
  outliers start: 119
  outliers final: 95
  residues processed: 279
  average time/residue: 0.2426
  time to fit residues: 101.3222
Evaluate side-chains
  278 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 104
    poor density    : 174
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   19 ASN
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  264 PHE
Chi-restraints excluded: chain B residue  276 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  408 MET
Chi-restraints excluded: chain B residue  418 THR
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue    8 GLU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  284 ASP
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  471 MET
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  541 THR
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  577 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 128 optimal weight:    0.0980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 549 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.148895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.119456 restraints weight = 17707.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.119570 restraints weight = 13859.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.120271 restraints weight = 12336.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13911  Z= 0.170
  Angle     :  0.563  11.409  18945  Z= 0.285
  Chirality :  0.044   0.268   2237
  Planarity :  0.004   0.048   2462
  Dihedral  :  9.981 175.436   2141
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.45 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 32.24 %
    Favored  : 61.51 %
  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:  0.28 (0.21), residues: 1776
  helix:  1.50 (0.22), residues: 564
  sheet: -0.08 (0.24), residues: 434
  loop : -0.56 (0.25), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.005   TRP B 173 
 HIS   0.002   0.000   HIS B 344 
 PHE   0.015   0.001   PHE B 416 
 TYR   0.013   0.001   TYR A 411 
 ARG   0.007   0.000   ARG C 517 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 195
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.6905 (t80)
REVERT: A  356 ARG cc_start: 0.7376 (mmm160) cc_final: 0.7094 (mmm160)
REVERT: A  420 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7028 (mp0)
REVERT: B   11 PHE cc_start: 0.4502 (m-80) cc_final: 0.4295 (m-80)
REVERT: B  222 GLN cc_start: 0.7733 (pp30) cc_final: 0.7089 (pt0)
REVERT: B  312 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6302 (ttp80)
REVERT: B  335 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8389 (mm)
REVERT: C  202 ILE cc_start: 0.8345 (mm) cc_final: 0.8056 (mm)
REVERT: C  344 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.5848 (t70)
REVERT: C  379 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8244 (m)
REVERT: C  524 ILE cc_start: 0.7883 (pt) cc_final: 0.7670 (pt)
REVERT: C  534 MET cc_start: 0.7272 (tmm) cc_final: 0.6928 (tmm)
  outliers start: 88
  outliers final: 63
  residues processed: 263
  average time/residue: 0.2486
  time to fit residues: 98.1545
Evaluate side-chains
  251 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 182
  time to evaluate  : 1.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  264 PHE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  440 ARG
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  543 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 152 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 141 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 151 optimal weight:    4.9990
   chunk 127 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 117 optimal weight:    0.7980
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 549 GLN
** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.145068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.115952 restraints weight = 17872.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.115225 restraints weight = 14361.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.115959 restraints weight = 12865.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  13911  Z= 0.348
  Angle     :  0.627  11.566  18945  Z= 0.319
  Chirality :  0.047   0.336   2237
  Planarity :  0.004   0.048   2462
  Dihedral  : 10.052 174.776   2141
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.24 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  7.39 %
    Allowed  : 31.25 %
    Favored  : 61.36 %
  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:  0.16 (0.21), residues: 1776
  helix:  1.32 (0.22), residues: 565
  sheet: -0.11 (0.24), residues: 433
  loop : -0.59 (0.25), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP B 173 
 HIS   0.003   0.001   HIS A 409 
 PHE   0.015   0.002   PHE B 416 
 TYR   0.017   0.002   TYR C 411 
 ARG   0.009   0.000   ARG A  84 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 104
    poor density    : 177
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6987 (t80)
REVERT: A  356 ARG cc_start: 0.7540 (mmm160) cc_final: 0.7233 (mmm160)
REVERT: A  420 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7116 (mp0)
REVERT: B   11 PHE cc_start: 0.4947 (m-80) cc_final: 0.4650 (m-80)
REVERT: B   61 ASN cc_start: 0.8028 (m-40) cc_final: 0.7022 (p0)
REVERT: B  222 GLN cc_start: 0.7788 (pp30) cc_final: 0.7161 (pt0)
REVERT: B  276 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5905 (m-80)
REVERT: B  312 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6379 (ttp80)
REVERT: B  355 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6891 (mp)
REVERT: C  202 ILE cc_start: 0.8394 (mm) cc_final: 0.8126 (mm)
REVERT: C  344 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.5892 (t70)
REVERT: C  379 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8384 (m)
REVERT: C  534 MET cc_start: 0.7303 (tmm) cc_final: 0.6987 (tmm)
  outliers start: 104
  outliers final: 79
  residues processed: 260
  average time/residue: 0.2468
  time to fit residues: 95.6314
Evaluate side-chains
  257 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 171
  time to evaluate  : 1.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  264 PHE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  276 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  557 ILE
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  543 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0980
   chunk 126 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 141 optimal weight:    6.9990
   chunk 156 optimal weight:   10.0000
   chunk 135 optimal weight:    0.0010
   chunk 74 optimal weight:    1.9990
   chunk 160 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8190

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.151690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.121831 restraints weight = 17335.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.122595 restraints weight = 13364.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.123385 restraints weight = 11328.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13911  Z= 0.176
  Angle     :  0.569  11.185  18945  Z= 0.289
  Chirality :  0.044   0.285   2237
  Planarity :  0.004   0.048   2462
  Dihedral  :  9.863 176.313   2141
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.39 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 32.60 %
    Favored  : 61.65 %
  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:  0.30 (0.21), residues: 1776
  helix:  1.47 (0.22), residues: 565
  sheet: -0.08 (0.24), residues: 438
  loop : -0.50 (0.25), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP B 173 
 HIS   0.002   0.000   HIS C 410 
 PHE   0.014   0.001   PHE B 416 
 TYR   0.012   0.001   TYR A 411 
 ARG   0.006   0.000   ARG C 517 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 196
  time to evaluate  : 1.606 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7786 (mmm)
REVERT: A  264 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6813 (t80)
REVERT: A  356 ARG cc_start: 0.7323 (mmm160) cc_final: 0.7040 (mmm160)
REVERT: A  402 GLU cc_start: 0.7868 (pm20) cc_final: 0.7602 (pt0)
REVERT: A  420 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7067 (mp0)
REVERT: B   11 PHE cc_start: 0.4424 (m-80) cc_final: 0.4223 (m-80)
REVERT: B   61 ASN cc_start: 0.7979 (m-40) cc_final: 0.6950 (p0)
REVERT: B  222 GLN cc_start: 0.7631 (pp30) cc_final: 0.7015 (pt0)
REVERT: B  312 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6344 (ttp80)
REVERT: B  355 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6764 (mp)
REVERT: C  202 ILE cc_start: 0.8218 (mm) cc_final: 0.7908 (mm)
REVERT: C  344 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.5840 (t70)
REVERT: C  379 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8224 (m)
REVERT: C  524 ILE cc_start: 0.7868 (pt) cc_final: 0.7639 (pt)
REVERT: C  534 MET cc_start: 0.7238 (tmm) cc_final: 0.6923 (tmm)
  outliers start: 81
  outliers final: 67
  residues processed: 258
  average time/residue: 0.2397
  time to fit residues: 92.6472
Evaluate side-chains
  256 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 182
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  264 PHE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  440 ARG
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  543 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 117 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   chunk 136 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 84 optimal weight:    9.9990
   chunk 143 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 138 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 549 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.146070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.115676 restraints weight = 17762.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.116227 restraints weight = 14137.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.117419 restraints weight = 12369.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  13911  Z= 0.339
  Angle     :  0.629  11.319  18945  Z= 0.320
  Chirality :  0.047   0.305   2237
  Planarity :  0.004   0.048   2462
  Dihedral  :  9.926 175.710   2141
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.01 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 32.24 %
    Favored  : 61.65 %
  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:  0.20 (0.21), residues: 1776
  helix:  1.33 (0.22), residues: 564
  sheet: -0.08 (0.24), residues: 434
  loop : -0.56 (0.25), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.005   TRP B 173 
 HIS   0.003   0.001   HIS A 409 
 PHE   0.016   0.002   PHE B 531 
 TYR   0.016   0.001   TYR C 411 
 ARG   0.009   0.000   ARG A  84 

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

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

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3552 Ramachandran restraints generated.
    1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 176
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6877 (t80)
REVERT: A  329 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6980 (mtm110)
REVERT: A  420 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7133 (mp0)
REVERT: A  523 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7375 (m-30)
REVERT: B   61 ASN cc_start: 0.7978 (m-40) cc_final: 0.6938 (p0)
REVERT: B  222 GLN cc_start: 0.7736 (pp30) cc_final: 0.7108 (pt0)
REVERT: B  276 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5942 (m-80)
REVERT: B  312 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6333 (ttp80)
REVERT: B  355 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6850 (mp)
REVERT: C  202 ILE cc_start: 0.8327 (mm) cc_final: 0.8042 (mm)
REVERT: C  344 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.5886 (t70)
REVERT: C  379 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8328 (m)
REVERT: C  497 MET cc_start: 0.8480 (mmm) cc_final: 0.8180 (mmm)
REVERT: C  534 MET cc_start: 0.7240 (tmm) cc_final: 0.6943 (tmm)
  outliers start: 86
  outliers final: 73
  residues processed: 242
  average time/residue: 0.2320
  time to fit residues: 84.7500
Evaluate side-chains
  253 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 172
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   51 MET
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  264 PHE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain B residue   47 ASP
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  276 TYR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  312 ARG
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  418 THR
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  465 SER
Chi-restraints excluded: chain B residue  473 SER
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  174 VAL
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 GLU
Chi-restraints excluded: chain C residue  243 LEU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  331 LEU
Chi-restraints excluded: chain C residue  344 HIS
Chi-restraints excluded: chain C residue  371 SER
Chi-restraints excluded: chain C residue  379 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  417 SER
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  477 SER
Chi-restraints excluded: chain C residue  492 VAL
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain C residue  541 THR
Chi-restraints excluded: chain C residue  543 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   chunk 118 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9980
   chunk 147 optimal weight:   20.0000
   chunk 106 optimal weight:    0.9990
   chunk 156 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 154 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0670
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
B 549 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.125982 restraints weight = 17128.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.128998 restraints weight = 12275.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.130045 restraints weight = 9932.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3303 r_free = 0.3303    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
r_final: 0.3303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13911  Z= 0.169
  Angle     :  0.575  10.732  18945  Z= 0.292
  Chirality :  0.044   0.268   2237
  Planarity :  0.004   0.047   2462
  Dihedral  :  9.772 177.271   2141
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.11 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 32.88 %
    Favored  : 61.65 %
  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:  0.34 (0.21), residues: 1776
  helix:  1.48 (0.22), residues: 564
  sheet: -0.00 (0.24), residues: 435
  loop : -0.49 (0.25), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.005   TRP B 173 
 HIS   0.002   0.001   HIS C 410 
 PHE   0.014   0.001   PHE B 416 
 TYR   0.012   0.001   TYR A 411 
 ARG   0.006   0.000   ARG A 329 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3816.98 seconds
wall clock time: 69 minutes 19.53 seconds (4159.53 seconds total)