Starting phenix.real_space_refine
on Tue Jul 29 11:15:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxf_40850/07_2025/8sxf_40850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxf_40850/07_2025/8sxf_40850.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxf_40850/07_2025/8sxf_40850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxf_40850/07_2025/8sxf_40850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxf_40850/07_2025/8sxf_40850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxf_40850/07_2025/8sxf_40850.cif"
  }
  resolution = 3.92
  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=   0.000 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    7074      2.51       5
     N    2013      2.21       5
     O    2217      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11321
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2733
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 20, 'TRANS': 343}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2707
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 20, 'TRANS': 340}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4248
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 512}
    Chain: "D"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 30
          Classifications: {'peptide': 6}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'TRANS': 5}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'UNK:plan-1': 6}
          Unresolved non-hydrogen planarities: 6
    Chain: "E"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1603
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 10, 'TRANS': 203}
          Chain breaks: 2
  Time building chain proxies: 7.06, per 1000 atoms: 0.62
  Number of scatterers: 11321
  At special positions: 0
  Unit cell: (91.908, 132.894, 182.574, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O    2217      8.00
     N    2013      7.00
     C    7074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2716

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 14 sheets defined
      56.2% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 60
    Processing helix  chain 'A' and resid 65 through 82
      removed outlier: 4.086A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 101
    Processing helix  chain 'A' and resid 127 through 132
      removed outlier: 3.814A  pdb=" N   ARG A 131 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 161
    Processing helix  chain 'A' and resid 214 through 230
    Processing helix  chain 'A' and resid 248 through 259
      removed outlier: 3.519A  pdb=" N   ALA A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 314
      removed outlier: 3.577A  pdb=" N   VAL A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.793A  pdb=" N   ARG A 340 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 417
      removed outlier: 4.231A  pdb=" N   SER A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 435
    Processing helix  chain 'B' and resid 42 through 59
    Processing helix  chain 'B' and resid 65 through 80
      removed outlier: 3.548A  pdb=" N   LEU B  69 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 98
      removed outlier: 3.548A  pdb=" N   GLU B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 132
    Processing helix  chain 'B' and resid 152 through 161
    Processing helix  chain 'B' and resid 214 through 231
    Processing helix  chain 'B' and resid 248 through 260
    Processing helix  chain 'B' and resid 272 through 276
      removed outlier: 3.601A  pdb=" N   GLU B 276 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 314
    Processing helix  chain 'B' and resid 412 through 417
      removed outlier: 4.063A  pdb=" N   ASP B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 435
    Processing helix  chain 'C' and resid 49 through 65
    Processing helix  chain 'C' and resid 67 through 83
      removed outlier: 3.535A  pdb=" N   ALA C  71 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 99
    Processing helix  chain 'C' and resid 100 through 115
    Processing helix  chain 'C' and resid 118 through 132
      removed outlier: 3.641A  pdb=" N   GLN C 122 " --> pdb=" O   ASN C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 148
    Processing helix  chain 'C' and resid 153 through 164
      removed outlier: 4.263A  pdb=" N   LEU C 157 " --> pdb=" O   HIS C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 183
    Processing helix  chain 'C' and resid 187 through 201
    Processing helix  chain 'C' and resid 203 through 213
      removed outlier: 3.556A  pdb=" N   ASN C 213 " --> pdb=" O   LEU C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 219
    Processing helix  chain 'C' and resid 220 through 234
    Processing helix  chain 'C' and resid 235 through 250
      removed outlier: 3.611A  pdb=" N   ALA C 239 " --> pdb=" O   ARG C 235 " (cutoff:3.500A)
      Proline residue:  C 241  - end of helix
    Processing helix  chain 'C' and resid 253 through 268
      removed outlier: 4.377A  pdb=" N   ARG C 257 " --> pdb=" O   ASP C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 284
    Processing helix  chain 'C' and resid 287 through 301
    Processing helix  chain 'C' and resid 303 through 318
    Processing helix  chain 'C' and resid 320 through 336
    Processing helix  chain 'C' and resid 337 through 348
      removed outlier: 3.503A  pdb=" N   TYR C 345 " --> pdb=" O   ALA C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 353 through 368
    Processing helix  chain 'C' and resid 370 through 385
      removed outlier: 3.874A  pdb=" N   GLN C 385 " --> pdb=" O   ALA C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 404
      removed outlier: 3.903A  pdb=" N   GLN C 391 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 420
    Processing helix  chain 'C' and resid 423 through 438
    Processing helix  chain 'C' and resid 439 through 454
      removed outlier: 4.626A  pdb=" N   MET C 443 " --> pdb=" O   ASP C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 472
    Processing helix  chain 'C' and resid 475 through 489
    Processing helix  chain 'C' and resid 492 through 507
      removed outlier: 3.544A  pdb=" N   LEU C 496 " --> pdb=" O   ASP C 492 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 509 through 523
    Processing helix  chain 'C' and resid 525 through 540
    Processing helix  chain 'C' and resid 541 through 556
      removed outlier: 4.211A  pdb=" N   ALA C 545 " --> pdb=" O   ARG C 541 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR C 552 " --> pdb=" O   ILE C 548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 570
    Processing helix  chain 'E' and resid 214 through 230
      removed outlier: 4.002A  pdb=" N   GLU E 218 " --> pdb=" O   ASN E 214 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 260
    Processing helix  chain 'E' and resid 302 through 314
    Processing helix  chain 'E' and resid 412 through 417
    Processing helix  chain 'E' and resid 417 through 434
    Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106
    Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 114
      removed outlier: 6.632A  pdb=" N   GLY A 112 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   VAL A 120 " --> pdb=" O   GLY A 112 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLU A 114 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   ILE A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147
      removed outlier: 5.145A  pdb=" N   ILE A 140 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 200
      removed outlier: 5.459A  pdb=" N   SER A 196 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   VAL A 198 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   TYR A 205 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ALA A 204 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ASP A 240 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU A 206 " --> pdb=" O   ASP A 240 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU A 292 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   MET A 320 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL A 294 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280
      removed outlier: 3.759A  pdb=" N   TYR A 267 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL A 330 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374
    Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 88
      removed outlier: 3.505A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88
      removed outlier: 3.505A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ARG B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL B 330 " --> pdb=" O   THR B 346 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.859A  pdb=" N   GLY B 162 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 114
      removed outlier: 6.891A  pdb=" N   GLU B 110 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 143
    Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 170
    Processing sheet with id=AB4, first strand: chain 'B' and resid 194 through 200
      removed outlier: 5.132A  pdb=" N   SER B 196 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG B 207 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   VAL B 198 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   TYR B 205 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU B 200 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 204 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP B 240 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 208 " --> pdb=" O   ASP B 240 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL B 293 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 8.848A  pdb=" N   MET B 320 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL B 294 " --> pdb=" O   MET B 320 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 198
      removed outlier: 3.836A  pdb=" N   ILE E 208 " --> pdb=" O   ASP E 240 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU E 237 " --> pdb=" O   VAL E 293 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   LEU E 295 " --> pdb=" O   LEU E 237 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   LEU E 239 " --> pdb=" O   LEU E 295 " (cutoff:3.500A)

    645 hydrogen bonds defined for protein.
    1884 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.62

  Time building geometry restraints manager: 3.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3946
        1.34 -     1.46: 1735
        1.46 -     1.57: 5769
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 11483
  Sorted by residual:
  bond pdb=" N   GLY B 247 "
       pdb=" CA  GLY B 247 "
    ideal  model  delta    sigma   weight residual
    1.458  1.447  0.010 9.20e-03 1.18e+04 1.28e+00
  bond pdb=" N   VAL B 290 "
       pdb=" CA  VAL B 290 "
    ideal  model  delta    sigma   weight residual
    1.468  1.460  0.008 1.05e-02 9.07e+03 5.84e-01
  bond pdb=" N   ILE B 140 "
       pdb=" CA  ILE B 140 "
    ideal  model  delta    sigma   weight residual
    1.474  1.463  0.012 1.57e-02 4.06e+03 5.59e-01
  bond pdb=" C   ILE A  74 "
       pdb=" O   ILE A  74 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.13e-02 7.83e+03 5.30e-01
  bond pdb=" N   ALA E 301 "
       pdb=" CA  ALA E 301 "
    ideal  model  delta    sigma   weight residual
    1.459  1.468 -0.009 1.20e-02 6.94e+03 5.28e-01
  ... (remaining 11478 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 14853
        1.00 -     2.01: 548
        2.01 -     3.01: 64
        3.01 -     4.02: 65
        4.02 -     5.02: 5
  Bond angle restraints: 15535
  Sorted by residual:
  angle pdb=" C   GLN B 358 "
        pdb=" N   ALA B 359 "
        pdb=" CA  ALA B 359 "
      ideal   model   delta    sigma   weight residual
     121.54  125.61   -4.07 1.91e+00 2.74e-01 4.54e+00
  angle pdb=" CA  TYR B 205 "
        pdb=" CB  TYR B 205 "
        pdb=" CG  TYR B 205 "
      ideal   model   delta    sigma   weight residual
     113.90  117.64   -3.74 1.80e+00 3.09e-01 4.31e+00
  angle pdb=" C   ASN A 338 "
        pdb=" N   ASP A 339 "
        pdb=" CA  ASP A 339 "
      ideal   model   delta    sigma   weight residual
     121.54  124.93   -3.39 1.91e+00 2.74e-01 3.15e+00
  angle pdb=" CA  VAL A 141 "
        pdb=" C   VAL A 141 "
        pdb=" N   GLN A 142 "
      ideal   model   delta    sigma   weight residual
     116.60  119.08   -2.48 1.45e+00 4.76e-01 2.92e+00
  angle pdb=" N   VAL A 141 "
        pdb=" CA  VAL A 141 "
        pdb=" C   VAL A 141 "
      ideal   model   delta    sigma   weight residual
     109.34  112.63   -3.29 2.08e+00 2.31e-01 2.51e+00
  ... (remaining 15530 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 6297
       17.76 -    35.52: 607
       35.52 -    53.28: 128
       53.28 -    71.04: 24
       71.04 -    88.80: 17
  Dihedral angle restraints: 7073
    sinusoidal: 2848
      harmonic: 4225
  Sorted by residual:
  dihedral pdb=" CA  PHE C  48 "
           pdb=" C   PHE C  48 "
           pdb=" N   SER C  49 "
           pdb=" CA  SER C  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.67   18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  SER E 300 "
           pdb=" C   SER E 300 "
           pdb=" N   ALA E 301 "
           pdb=" CA  ALA E 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.19  -16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ASP B 115 "
           pdb=" CB  ASP B 115 "
           pdb=" CG  ASP B 115 "
           pdb=" OD1 ASP B 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.94   56.94     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 7070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1158
       0.027 -    0.054: 390
       0.054 -    0.081: 88
       0.081 -    0.108: 85
       0.108 -    0.135: 42
  Chirality restraints: 1763
  Sorted by residual:
  chirality pdb=" CA  ILE E 318 "
            pdb=" N   ILE E 318 "
            pdb=" C   ILE E 318 "
            pdb=" CB  ILE E 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE E 296 "
            pdb=" N   ILE E 296 "
            pdb=" C   ILE E 296 "
            pdb=" CB  ILE E 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  ILE A 109 "
            pdb=" N   ILE A 109 "
            pdb=" C   ILE A 109 "
            pdb=" CB  ILE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1760 not shown)

  Planarity restraints: 2074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 285 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO E 286 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO E 286 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 286 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 127 "    0.020 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO B 128 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 128 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 128 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 205 "    0.012 2.00e-02 2.50e+03   8.30e-03 1.38e+00
        pdb=" CG  TYR B 205 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 205 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 205 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 205 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 205 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 205 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 205 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2071 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 224
        2.63 -     3.20: 11375
        3.20 -     3.77: 18131
        3.77 -     4.33: 23765
        4.33 -     4.90: 38773
  Nonbonded interactions: 92268
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 229 "
            pdb=" OG  SER C 232 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" O   LEU C 468 "
            pdb=" OG1 THR C 472 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" OE2 GLU E 305 "
            pdb=" OG  SER E 324 "
     model   vdw
     2.077 3.040
  nonbonded pdb=" OG1 THR C  82 "
            pdb=" OD1 ASP C  84 "
     model   vdw
     2.091 3.040
  nonbonded pdb=" OD1 ASP C 379 "
            pdb=" OH  TYR C 393 "
     model   vdw
     2.098 3.040
  ... (remaining 92263 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 38 through 371 or resid 411 through 436))
  selection = (chain 'B' and (resid 38 through 371 or resid 411 through 436))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.560
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11483  Z= 0.107
  Angle     :  0.482   5.022  15535  Z= 0.250
  Chirality :  0.038   0.135   1763
  Planarity :  0.003   0.039   2074
  Dihedral  : 15.077  88.795   4357
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  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:  1.25 (0.22), residues: 1455
  helix:  2.04 (0.19), residues: 754
  sheet: -0.54 (0.42), residues: 161
  loop : -0.43 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 537 
 HIS   0.004   0.001   HIS C 531 
 PHE   0.008   0.001   PHE A 325 
 TYR   0.020   0.001   TYR B 205 
 ARG   0.002   0.000   ARG B 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13597 (  642)
  hydrogen bonds       : angle       5.69141 ( 1884)
  covalent geometry    : bond        0.00223 (11483)
  covalent geometry    : angle       0.48194 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 LEU cc_start: 0.8598 (tp) cc_final: 0.8079 (pp)
REVERT: E  233 ARG cc_start: 0.6092 (tpm170) cc_final: 0.5743 (mmm160)
REVERT: E  385 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6446 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.2638
  time to fit residues: 42.9037
Evaluate side-chains
  68 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    0.0170
   chunk 110 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   chunk 37 optimal weight:    0.3980
   chunk 74 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 114 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 69 optimal weight:    0.2980
   chunk 85 optimal weight:    0.9990
   chunk 132 optimal weight:    0.4980
   overall best weight:    0.2596

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

Flipped N/Q/H residues before XYZ refinement:
C 218 HIS
C 486 HIS
E 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.136812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.112888 restraints weight = 33188.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.110462 restraints weight = 47217.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.111849 restraints weight = 41805.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  11483  Z= 0.130
  Angle     :  0.586   7.454  15535  Z= 0.296
  Chirality :  0.041   0.204   1763
  Planarity :  0.004   0.047   2074
  Dihedral  :  4.042  19.955   1606
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.05 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.22), residues: 1455
  helix:  1.84 (0.18), residues: 780
  sheet: -0.57 (0.42), residues: 159
  loop : -0.25 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 531 
 PHE   0.011   0.001   PHE A 325 
 TYR   0.018   0.001   TYR B 205 
 ARG   0.004   0.000   ARG B 186 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  642)
  hydrogen bonds       : angle       4.44510 ( 1884)
  covalent geometry    : bond        0.00276 (11483)
  covalent geometry    : angle       0.58584 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  259 PHE cc_start: 0.6683 (m-80) cc_final: 0.6204 (m-10)
REVERT: C  376 GLN cc_start: 0.7068 (pp30) cc_final: 0.6737 (pp30)
REVERT: E  214 ASN cc_start: 0.8146 (m-40) cc_final: 0.7887 (t0)
REVERT: E  226 LEU cc_start: 0.7174 (tp) cc_final: 0.6902 (tt)
REVERT: E  233 ARG cc_start: 0.6112 (tpm170) cc_final: 0.5844 (mmm160)
REVERT: E  385 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6580 (mm-30)
  outliers start: 20
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2628
  time to fit residues: 37.4718
Evaluate side-chains
  79 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  249 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 107 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 142 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 127 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.135370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.112969 restraints weight = 33824.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.112525 restraints weight = 56490.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.113254 restraints weight = 47745.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11483  Z= 0.143
  Angle     :  0.569   7.797  15535  Z= 0.284
  Chirality :  0.040   0.148   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  4.067  20.050   1606
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.98 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.22), residues: 1455
  helix:  1.75 (0.18), residues: 784
  sheet: -0.68 (0.41), residues: 171
  loop : -0.25 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 501 
 HIS   0.003   0.001   HIS C 531 
 PHE   0.010   0.001   PHE A 325 
 TYR   0.021   0.001   TYR B 205 
 ARG   0.004   0.000   ARG E 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  642)
  hydrogen bonds       : angle       4.28749 ( 1884)
  covalent geometry    : bond        0.00327 (11483)
  covalent geometry    : angle       0.56894 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8233 (tt)
REVERT: A  424 LEU cc_start: 0.8539 (tp) cc_final: 0.8292 (pp)
REVERT: B   77 MET cc_start: 0.8375 (ttp) cc_final: 0.7886 (ptt)
REVERT: C  376 GLN cc_start: 0.6966 (pp30) cc_final: 0.6711 (pp30)
REVERT: E  214 ASN cc_start: 0.8309 (m-40) cc_final: 0.8062 (t0)
REVERT: E  381 GLU cc_start: 0.7489 (tp30) cc_final: 0.7259 (tp30)
REVERT: E  385 GLU cc_start: 0.7872 (mm-30) cc_final: 0.6849 (mm-30)
  outliers start: 22
  outliers final: 11
  residues processed: 100
  average time/residue: 0.2495
  time to fit residues: 36.9732
Evaluate side-chains
  81 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 129 optimal weight:    0.0770
   chunk 91 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
B  84 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.137744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.116426 restraints weight = 33683.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.117838 restraints weight = 57258.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.117959 restraints weight = 40299.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11483  Z= 0.156
  Angle     :  0.575  12.433  15535  Z= 0.285
  Chirality :  0.040   0.148   1763
  Planarity :  0.004   0.052   2074
  Dihedral  :  4.102  20.571   1606
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.83 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.22), residues: 1455
  helix:  1.75 (0.18), residues: 782
  sheet: -0.66 (0.41), residues: 171
  loop : -0.29 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.010   0.001   PHE A 325 
 TYR   0.021   0.002   TYR B 205 
 ARG   0.003   0.000   ARG E 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03632 (  642)
  hydrogen bonds       : angle       4.20801 ( 1884)
  covalent geometry    : bond        0.00358 (11483)
  covalent geometry    : angle       0.57517 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8197 (tt)
REVERT: A  199 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7600 (mp)
REVERT: A  424 LEU cc_start: 0.8521 (tp) cc_final: 0.8147 (pp)
REVERT: B   77 MET cc_start: 0.8347 (ttp) cc_final: 0.7979 (ptt)
REVERT: C  376 GLN cc_start: 0.6998 (pp30) cc_final: 0.6748 (pp30)
REVERT: E  214 ASN cc_start: 0.8303 (m-40) cc_final: 0.8057 (t0)
REVERT: E  385 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7023 (mm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 100
  average time/residue: 0.2314
  time to fit residues: 34.1124
Evaluate side-chains
  86 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  349 TYR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 50 optimal weight:    0.1980
   chunk 99 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
E 212 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.133412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.110065 restraints weight = 33313.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.109053 restraints weight = 55559.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.109870 restraints weight = 48162.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11483  Z= 0.197
  Angle     :  0.609  12.273  15535  Z= 0.302
  Chirality :  0.041   0.149   1763
  Planarity :  0.004   0.055   2074
  Dihedral  :  4.261  22.311   1606
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.58 %
    Favored  : 80.40 %
  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:  0.94 (0.22), residues: 1455
  helix:  1.61 (0.18), residues: 783
  sheet: -0.69 (0.41), residues: 171
  loop : -0.37 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 549 
 HIS   0.004   0.001   HIS C 526 
 PHE   0.025   0.001   PHE E 325 
 TYR   0.022   0.002   TYR B 205 
 ARG   0.003   0.000   ARG E 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03826 (  642)
  hydrogen bonds       : angle       4.28563 ( 1884)
  covalent geometry    : bond        0.00455 (11483)
  covalent geometry    : angle       0.60930 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8304 (tt)
REVERT: A  199 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7492 (mp)
REVERT: B   77 MET cc_start: 0.8473 (ttp) cc_final: 0.8179 (ptt)
REVERT: C  376 GLN cc_start: 0.7094 (pp30) cc_final: 0.6781 (pp30)
REVERT: E  212 GLN cc_start: 0.5623 (OUTLIER) cc_final: 0.5298 (pp30)
REVERT: E  385 GLU cc_start: 0.8081 (mm-30) cc_final: 0.6983 (mm-30)
  outliers start: 36
  outliers final: 20
  residues processed: 103
  average time/residue: 0.2150
  time to fit residues: 33.6483
Evaluate side-chains
  90 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  349 TYR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain E residue  212 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 128 optimal weight:    0.0370
   chunk 54 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 138 optimal weight:    0.3980
   chunk 124 optimal weight:    0.4980
   chunk 144 optimal weight:    0.2980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.4300 r_free = 0.4300 target = 0.136446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.111993 restraints weight = 33712.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.109695 restraints weight = 42547.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.111067 restraints weight = 38160.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11483  Z= 0.112
  Angle     :  0.557  13.388  15535  Z= 0.278
  Chirality :  0.040   0.147   1763
  Planarity :  0.004   0.054   2074
  Dihedral  :  4.014  19.598   1606
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.17 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.22), residues: 1455
  helix:  1.74 (0.18), residues: 784
  sheet: -0.49 (0.43), residues: 159
  loop : -0.38 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 501 
 HIS   0.006   0.001   HIS C 526 
 PHE   0.018   0.001   PHE C 191 
 TYR   0.019   0.001   TYR B 418 
 ARG   0.005   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  642)
  hydrogen bonds       : angle       4.08470 ( 1884)
  covalent geometry    : bond        0.00245 (11483)
  covalent geometry    : angle       0.55721 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 1.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8402 (tt)
REVERT: B   77 MET cc_start: 0.8195 (ttp) cc_final: 0.7725 (ptt)
REVERT: C  376 GLN cc_start: 0.7211 (pp30) cc_final: 0.6893 (pp30)
REVERT: E  385 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6740 (mm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 110
  average time/residue: 0.2252
  time to fit residues: 36.4243
Evaluate side-chains
  89 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 69 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 133 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 123 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0370
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
C 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.135926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.111572 restraints weight = 33790.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.108664 restraints weight = 46667.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.110249 restraints weight = 40100.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11483  Z= 0.126
  Angle     :  0.581  13.189  15535  Z= 0.288
  Chirality :  0.041   0.185   1763
  Planarity :  0.004   0.052   2074
  Dihedral  :  3.957  19.680   1606
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.43 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.22), residues: 1455
  helix:  1.76 (0.18), residues: 784
  sheet: -0.60 (0.41), residues: 169
  loop : -0.38 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.020   0.001   PHE C 191 
 TYR   0.016   0.001   TYR B 205 
 ARG   0.004   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03378 (  642)
  hydrogen bonds       : angle       4.05337 ( 1884)
  covalent geometry    : bond        0.00287 (11483)
  covalent geometry    : angle       0.58122 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8310 (tt)
REVERT: B  259 PHE cc_start: 0.6623 (m-80) cc_final: 0.6112 (m-80)
REVERT: B  422 GLN cc_start: 0.7376 (mm110) cc_final: 0.7172 (mm110)
REVERT: C  376 GLN cc_start: 0.7251 (pp30) cc_final: 0.6988 (pp30)
REVERT: E  377 ARG cc_start: 0.6056 (mmp80) cc_final: 0.5516 (mmp80)
REVERT: E  385 GLU cc_start: 0.7775 (mm-30) cc_final: 0.6754 (mm-30)
  outliers start: 31
  outliers final: 22
  residues processed: 102
  average time/residue: 0.2384
  time to fit residues: 35.5463
Evaluate side-chains
  97 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  214 ASN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 50 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   chunk 109 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 125 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.135356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.113679 restraints weight = 33725.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.112584 restraints weight = 57378.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.113590 restraints weight = 53169.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11483  Z= 0.141
  Angle     :  0.583  13.637  15535  Z= 0.288
  Chirality :  0.041   0.178   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  4.013  19.687   1606
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.43 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.22), residues: 1455
  helix:  1.75 (0.18), residues: 785
  sheet: -0.71 (0.41), residues: 164
  loop : -0.42 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.022   0.001   PHE C 191 
 TYR   0.023   0.001   TYR B 418 
 ARG   0.007   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  642)
  hydrogen bonds       : angle       4.08072 ( 1884)
  covalent geometry    : bond        0.00326 (11483)
  covalent geometry    : angle       0.58266 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 72
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8216 (tt)
REVERT: B  259 PHE cc_start: 0.6673 (m-80) cc_final: 0.6164 (m-80)
REVERT: C  376 GLN cc_start: 0.7133 (pp30) cc_final: 0.6918 (pp30)
REVERT: E  385 GLU cc_start: 0.7896 (mm-30) cc_final: 0.6754 (mm-30)
  outliers start: 32
  outliers final: 24
  residues processed: 99
  average time/residue: 0.2146
  time to fit residues: 31.9083
Evaluate side-chains
  95 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  214 ASN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 145 optimal weight:    0.6980
   chunk 100 optimal weight:   10.0000
   chunk 124 optimal weight:    0.0000
   chunk 49 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 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 = 0.4294 r_free = 0.4294 target = 0.135619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.113396 restraints weight = 33876.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.112868 restraints weight = 58048.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.113617 restraints weight = 50052.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11483  Z= 0.123
  Angle     :  0.566  14.054  15535  Z= 0.280
  Chirality :  0.040   0.172   1763
  Planarity :  0.004   0.052   2074
  Dihedral  :  3.944  19.204   1606
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.01 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.22), residues: 1455
  helix:  1.77 (0.18), residues: 784
  sheet: -0.69 (0.42), residues: 158
  loop : -0.41 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.021   0.001   PHE C 191 
 TYR   0.016   0.001   TYR B 205 
 ARG   0.006   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  642)
  hydrogen bonds       : angle       4.03427 ( 1884)
  covalent geometry    : bond        0.00279 (11483)
  covalent geometry    : angle       0.56612 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 1.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8229 (tt)
REVERT: B  259 PHE cc_start: 0.6516 (m-80) cc_final: 0.5954 (m-80)
REVERT: E  385 GLU cc_start: 0.7816 (mm-30) cc_final: 0.6794 (mm-30)
  outliers start: 28
  outliers final: 23
  residues processed: 94
  average time/residue: 0.2417
  time to fit residues: 36.4151
Evaluate side-chains
  91 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 1.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  214 ASN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 125 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   chunk 66 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 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 = 0.4292 r_free = 0.4292 target = 0.135476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.113383 restraints weight = 33665.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.112233 restraints weight = 57161.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.113472 restraints weight = 49850.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11483  Z= 0.128
  Angle     :  0.575  14.309  15535  Z= 0.286
  Chirality :  0.040   0.160   1763
  Planarity :  0.004   0.052   2074
  Dihedral  :  3.961  19.095   1606
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.10 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.22), residues: 1455
  helix:  1.74 (0.18), residues: 785
  sheet: -0.68 (0.41), residues: 164
  loop : -0.38 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.021   0.001   PHE C 191 
 TYR   0.026   0.001   TYR B 418 
 ARG   0.006   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  642)
  hydrogen bonds       : angle       4.05384 ( 1884)
  covalent geometry    : bond        0.00294 (11483)
  covalent geometry    : angle       0.57547 (15535)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 1.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8236 (tt)
REVERT: B  259 PHE cc_start: 0.6354 (m-80) cc_final: 0.5819 (m-80)
REVERT: B  422 GLN cc_start: 0.7648 (mm110) cc_final: 0.7293 (mm110)
REVERT: E  385 GLU cc_start: 0.7822 (mm-30) cc_final: 0.6695 (mm-30)
  outliers start: 26
  outliers final: 23
  residues processed: 92
  average time/residue: 0.2686
  time to fit residues: 38.7403
Evaluate side-chains
  92 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  214 ASN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 120 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 131 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 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 = 0.4318 r_free = 0.4318 target = 0.138472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.116135 restraints weight = 33798.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.115836 restraints weight = 57136.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.116494 restraints weight = 50338.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11483  Z= 0.143
  Angle     :  0.581  14.478  15535  Z= 0.289
  Chirality :  0.041   0.208   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  4.000  19.861   1606
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.35 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.22), residues: 1455
  helix:  1.68 (0.18), residues: 786
  sheet: -0.70 (0.41), residues: 164
  loop : -0.42 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.025   0.001   PHE C 191 
 TYR   0.019   0.001   TYR B 205 
 ARG   0.006   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  642)
  hydrogen bonds       : angle       4.11383 ( 1884)
  covalent geometry    : bond        0.00330 (11483)
  covalent geometry    : angle       0.58134 (15535)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3538.28 seconds
wall clock time: 63 minutes 54.86 seconds (3834.86 seconds total)