Starting phenix.real_space_refine
on Sat Aug 23 09:52:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxf_40850/08_2025/8sxf_40850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxf_40850/08_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_40850/08_2025/8sxf_40850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxf_40850/08_2025/8sxf_40850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxf_40850/08_2025/8sxf_40850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxf_40850/08_2025/8sxf_40850.cif"
  }
  resolution = 3.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.42, per 1000 atoms: 0.21
  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: 1.07
  Conformation dependent library (CDL) restraints added in 413.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.34
  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: 1.30

  Time building geometry restraints manager: 1.41 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:             1.970
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.980
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (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
 ARG   0.002   0.000   ARG B 242 
 TYR   0.020   0.001   TYR B 205 
 PHE   0.008   0.001   PHE A 325 
 TRP   0.008   0.001   TRP C 537 
 HIS   0.004   0.001   HIS C 531 

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

*********************** 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  : 0.392 
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: 0.1121
  time to fit residues: 18.0382
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  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
C  64 GLN
C 218 HIS
E 212 GLN
E 230 ASN
E 422 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.130888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.106243 restraints weight = 33639.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.106477 restraints weight = 53380.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.107194 restraints weight = 41425.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.108235 restraints weight = 25105.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.108452 restraints weight = 21407.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11483  Z= 0.276
  Angle     :  0.718   9.783  15535  Z= 0.358
  Chirality :  0.044   0.151   1763
  Planarity :  0.005   0.057   2074
  Dihedral  :  4.633  22.502   1606
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.90 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.22), residues: 1455
  helix:  1.34 (0.18), residues: 784
  sheet: -0.64 (0.43), residues: 157
  loop : -0.60 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 186 
 TYR   0.027   0.002   TYR B 205 
 PHE   0.015   0.002   PHE A 325 
 TRP   0.013   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 (11483)
  covalent geometry    : angle       0.71781 (15535)
  hydrogen bonds       : bond        0.04655 (  642)
  hydrogen bonds       : angle       4.82781 ( 1884)

*********************** 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
  112 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8241 (ptm)
REVERT: C  376 GLN cc_start: 0.7240 (pp30) cc_final: 0.6915 (pp30)
REVERT: C  514 ARG cc_start: 0.6973 (ptt180) cc_final: 0.6010 (tpp-160)
REVERT: E  212 GLN cc_start: 0.5657 (OUTLIER) cc_final: 0.5089 (pp30)
REVERT: E  385 GLU cc_start: 0.8159 (mm-30) cc_final: 0.6921 (mm-30)
  outliers start: 28
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0960
  time to fit residues: 14.4009
Evaluate side-chains
  81 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue   77 MET
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   77 MET
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain E residue  212 GLN
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  306 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 135 optimal weight:    0.7980
   chunk 121 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
E 422 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.133138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.109059 restraints weight = 33745.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.108917 restraints weight = 49589.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.109685 restraints weight = 42348.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.110708 restraints weight = 25502.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.110928 restraints weight = 21877.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11483  Z= 0.154
  Angle     :  0.600   8.561  15535  Z= 0.300
  Chirality :  0.041   0.147   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  4.315  19.877   1606
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.66 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.22), residues: 1455
  helix:  1.52 (0.18), residues: 784
  sheet: -0.63 (0.43), residues: 159
  loop : -0.49 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 186 
 TYR   0.025   0.002   TYR B 205 
 PHE   0.009   0.001   PHE A 325 
 TRP   0.013   0.002   TRP C 501 
 HIS   0.003   0.001   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (11483)
  covalent geometry    : angle       0.59996 (15535)
  hydrogen bonds       : bond        0.03816 (  642)
  hydrogen bonds       : angle       4.45940 ( 1884)

*********************** 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
  103 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 75
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8236 (tt)
REVERT: B   77 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7787 (ptm)
REVERT: C  376 GLN cc_start: 0.7011 (pp30) cc_final: 0.6709 (pp30)
REVERT: C  406 GLN cc_start: 0.5040 (OUTLIER) cc_final: 0.4801 (mm-40)
REVERT: E  214 ASN cc_start: 0.7984 (m-40) cc_final: 0.7756 (t0)
REVERT: E  385 GLU cc_start: 0.8101 (mm-30) cc_final: 0.6977 (mm-30)
  outliers start: 28
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0848
  time to fit residues: 12.1379
Evaluate side-chains
  79 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  406 GLN
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  306 ILE
Chi-restraints excluded: chain E residue  351 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 40 optimal weight:    0.0370
   chunk 63 optimal weight:    0.5980
   chunk 12 optimal weight:   10.0000
   chunk 84 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 143 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
B  84 HIS
** C  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 422 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.138250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.115931 restraints weight = 34117.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.114838 restraints weight = 59649.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.115651 restraints weight = 51246.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.117356 restraints weight = 32511.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.117443 restraints weight = 21656.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11483  Z= 0.127
  Angle     :  0.555   7.966  15535  Z= 0.279
  Chirality :  0.040   0.200   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  4.161  20.508   1606
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.00 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.22), residues: 1455
  helix:  1.63 (0.18), residues: 784
  sheet: -0.61 (0.43), residues: 158
  loop : -0.47 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 227 
 TYR   0.021   0.001   TYR B 205 
 PHE   0.013   0.001   PHE C 191 
 TRP   0.011   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11483)
  covalent geometry    : angle       0.55539 (15535)
  hydrogen bonds       : bond        0.03529 (  642)
  hydrogen bonds       : angle       4.25181 ( 1884)

*********************** 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
  103 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8059 (tt)
REVERT: C  139 MET cc_start: 0.6814 (ttt) cc_final: 0.6560 (ttt)
REVERT: C  376 GLN cc_start: 0.7088 (pp30) cc_final: 0.6784 (pp30)
REVERT: C  406 GLN cc_start: 0.4987 (OUTLIER) cc_final: 0.4757 (mm-40)
REVERT: E  385 GLU cc_start: 0.7944 (mm-30) cc_final: 0.6820 (mm-30)
  outliers start: 29
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0824
  time to fit residues: 11.9351
Evaluate side-chains
  87 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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  171 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  373 VAL
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  306 ILE
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  406 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  249 LEU
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 24 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 110 optimal weight:    9.9990
   chunk 120 optimal weight:    5.9990
   chunk 138 optimal weight:    0.9980
   chunk 133 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 45 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0770
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** C  64 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 = 0.4324 r_free = 0.4324 target = 0.138912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.116188 restraints weight = 33692.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.116740 restraints weight = 58957.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.117309 restraints weight = 48653.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.118914 restraints weight = 30519.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.118904 restraints weight = 20924.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2346

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= 0.124
  Angle     :  0.540   7.580  15535  Z= 0.272
  Chirality :  0.040   0.161   1763
  Planarity :  0.004   0.053   2074
  Dihedral  :  4.025  18.257   1606
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.59 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.22), residues: 1455
  helix:  1.70 (0.18), residues: 785
  sheet: -0.83 (0.43), residues: 152
  loop : -0.40 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 186 
 TYR   0.020   0.001   TYR B 205 
 PHE   0.024   0.001   PHE E 325 
 TRP   0.011   0.002   TRP C 501 
 HIS   0.003   0.001   HIS C 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11483)
  covalent geometry    : angle       0.54005 (15535)
  hydrogen bonds       : bond        0.03412 (  642)
  hydrogen bonds       : angle       4.13320 ( 1884)

*********************** 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
  110 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8081 (tt)
REVERT: C  376 GLN cc_start: 0.7078 (pp30) cc_final: 0.6769 (pp30)
REVERT: C  406 GLN cc_start: 0.4959 (OUTLIER) cc_final: 0.4731 (mm-40)
REVERT: E  385 GLU cc_start: 0.7882 (mm-30) cc_final: 0.6804 (mm-30)
  outliers start: 32
  outliers final: 21
  residues processed: 106
  average time/residue: 0.1009
  time to fit residues: 16.2865
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  : 0.419 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue   77 MET
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  306 ILE
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  406 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  251 SER
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 95 optimal weight:    0.6980
   chunk 141 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.133909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.109344 restraints weight = 33944.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.108598 restraints weight = 48841.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.109453 restraints weight = 45943.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.110700 restraints weight = 26720.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.110863 restraints weight = 22228.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11483  Z= 0.148
  Angle     :  0.561   8.451  15535  Z= 0.282
  Chirality :  0.040   0.146   1763
  Planarity :  0.004   0.052   2074
  Dihedral  :  4.099  19.337   1606
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.09 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.22), residues: 1455
  helix:  1.68 (0.18), residues: 785
  sheet: -0.78 (0.42), residues: 156
  loop : -0.46 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 227 
 TYR   0.021   0.001   TYR B 205 
 PHE   0.013   0.001   PHE C 191 
 TRP   0.012   0.002   TRP C 304 
 HIS   0.007   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11483)
  covalent geometry    : angle       0.56101 (15535)
  hydrogen bonds       : bond        0.03510 (  642)
  hydrogen bonds       : angle       4.11511 ( 1884)

*********************** 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
  106 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 68
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8093 (tt)
REVERT: C  376 GLN cc_start: 0.7181 (pp30) cc_final: 0.6839 (pp30)
REVERT: C  406 GLN cc_start: 0.5617 (OUTLIER) cc_final: 0.5248 (mm-40)
REVERT: E  385 GLU cc_start: 0.7965 (mm-30) cc_final: 0.6827 (mm-30)
  outliers start: 38
  outliers final: 23
  residues processed: 101
  average time/residue: 0.0874
  time to fit residues: 13.8606
Evaluate side-chains
  91 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue   77 MET
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  306 ILE
Chi-restraints excluded: chain B residue  332 THR
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  406 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  251 SER
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 136 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9980
   chunk 138 optimal weight:    0.0570
   chunk 79 optimal weight:    0.0870
   chunk 118 optimal weight:    8.9990
   chunk 94 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.5076

-------------------------------------------------------------------------------
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  64 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 = 0.4300 r_free = 0.4300 target = 0.136362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.112546 restraints weight = 33613.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.111376 restraints weight = 49656.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.112238 restraints weight = 45118.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.113976 restraints weight = 28540.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.114202 restraints weight = 19519.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11483  Z= 0.116
  Angle     :  0.554  11.950  15535  Z= 0.276
  Chirality :  0.040   0.175   1763
  Planarity :  0.004   0.052   2074
  Dihedral  :  3.968  19.994   1606
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.76 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.22), residues: 1455
  helix:  1.75 (0.18), residues: 784
  sheet: -0.68 (0.44), residues: 143
  loop : -0.50 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 227 
 TYR   0.019   0.001   TYR B 205 
 PHE   0.018   0.001   PHE C 191 
 TRP   0.012   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11483)
  covalent geometry    : angle       0.55375 (15535)
  hydrogen bonds       : bond        0.03323 (  642)
  hydrogen bonds       : angle       4.05220 ( 1884)

*********************** 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
  107 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8281 (tt)
REVERT: B  259 PHE cc_start: 0.6615 (m-80) cc_final: 0.6038 (m-80)
REVERT: C  376 GLN cc_start: 0.7128 (pp30) cc_final: 0.6829 (pp30)
REVERT: C  406 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.5175 (mm-40)
REVERT: E  385 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6884 (mm-30)
  outliers start: 34
  outliers final: 24
  residues processed: 102
  average time/residue: 0.0913
  time to fit residues: 14.4486
Evaluate side-chains
  93 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue   77 MET
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  306 ILE
Chi-restraints excluded: chain B residue  332 THR
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  406 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  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 32 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0040
   chunk 34 optimal weight:    0.0370
   chunk 86 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 129 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.5070

-------------------------------------------------------------------------------
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  64 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 = 0.4297 r_free = 0.4297 target = 0.135992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.113443 restraints weight = 33649.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.112337 restraints weight = 52399.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.113493 restraints weight = 50433.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.113702 restraints weight = 30538.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.114250 restraints weight = 27205.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2782

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= 0.117
  Angle     :  0.550  11.593  15535  Z= 0.276
  Chirality :  0.040   0.153   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  3.952  19.147   1606
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.22), residues: 1455
  helix:  1.77 (0.18), residues: 784
  sheet: -0.68 (0.44), residues: 144
  loop : -0.46 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 233 
 TYR   0.023   0.001   TYR B 418 
 PHE   0.015   0.001   PHE C 191 
 TRP   0.014   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (11483)
  covalent geometry    : angle       0.55045 (15535)
  hydrogen bonds       : bond        0.03265 (  642)
  hydrogen bonds       : angle       4.01749 ( 1884)

*********************** 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
  98 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8332 (tt)
REVERT: B  259 PHE cc_start: 0.6570 (m-80) cc_final: 0.5931 (m-80)
REVERT: C  406 GLN cc_start: 0.5387 (OUTLIER) cc_final: 0.5108 (mm-40)
REVERT: E  385 GLU cc_start: 0.7790 (mm-30) cc_final: 0.6862 (mm-30)
  outliers start: 30
  outliers final: 25
  residues processed: 93
  average time/residue: 0.0802
  time to fit residues: 11.9068
Evaluate side-chains
  93 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue   77 MET
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  306 ILE
Chi-restraints excluded: chain B residue  332 THR
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  406 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  251 SER
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 123 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   chunk 114 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0870
   chunk 120 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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  64 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 = 0.4299 r_free = 0.4299 target = 0.136027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.113713 restraints weight = 33685.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.112151 restraints weight = 54301.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.113407 restraints weight = 46403.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.113809 restraints weight = 28844.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.114166 restraints weight = 26883.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2860

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= 0.119
  Angle     :  0.553  11.842  15535  Z= 0.278
  Chirality :  0.040   0.144   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  3.924  19.005   1606
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.68 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.22), residues: 1455
  helix:  1.77 (0.18), residues: 785
  sheet: -0.66 (0.45), residues: 144
  loop : -0.44 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 227 
 TYR   0.019   0.001   TYR B 205 
 PHE   0.016   0.001   PHE C 191 
 TRP   0.015   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11483)
  covalent geometry    : angle       0.55292 (15535)
  hydrogen bonds       : bond        0.03276 (  642)
  hydrogen bonds       : angle       4.01921 ( 1884)

*********************** 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
  97 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8364 (tt)
REVERT: B  259 PHE cc_start: 0.6649 (m-80) cc_final: 0.6012 (m-80)
REVERT: C  406 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.5207 (mm-40)
REVERT: E  385 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6864 (mm-30)
  outliers start: 30
  outliers final: 24
  residues processed: 92
  average time/residue: 0.0826
  time to fit residues: 11.8633
Evaluate side-chains
  92 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  209 THR
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  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  406 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  251 SER
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 96 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 63 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 29 optimal weight:    0.1980
   chunk 60 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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  64 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 = 0.4302 r_free = 0.4302 target = 0.136612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.113901 restraints weight = 33637.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.112871 restraints weight = 53254.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.113770 restraints weight = 48094.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.114294 restraints weight = 28391.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.114472 restraints weight = 28567.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.2920

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= 0.118
  Angle     :  0.549  12.175  15535  Z= 0.275
  Chirality :  0.040   0.154   1763
  Planarity :  0.004   0.050   2074
  Dihedral  :  3.904  18.611   1606
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.22), residues: 1455
  helix:  1.76 (0.18), residues: 785
  sheet: -0.62 (0.45), residues: 144
  loop : -0.42 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 227 
 TYR   0.026   0.001   TYR B 418 
 PHE   0.016   0.001   PHE C 191 
 TRP   0.022   0.002   TRP C 501 
 HIS   0.004   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (11483)
  covalent geometry    : angle       0.54899 (15535)
  hydrogen bonds       : bond        0.03271 (  642)
  hydrogen bonds       : angle       4.00381 ( 1884)

********************** 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
  97 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8407 (tt)
REVERT: B  259 PHE cc_start: 0.6654 (m-80) cc_final: 0.6011 (m-80)
REVERT: B  422 GLN cc_start: 0.7699 (mm110) cc_final: 0.7367 (mm110)
REVERT: C  406 GLN cc_start: 0.5505 (OUTLIER) cc_final: 0.5183 (mm-40)
REVERT: E  385 GLU cc_start: 0.7783 (mm-30) cc_final: 0.6797 (mm-30)
  outliers start: 28
  outliers final: 24
  residues processed: 92
  average time/residue: 0.0973
  time to fit residues: 13.4770
Evaluate side-chains
  93 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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  238 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  209 THR
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  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  406 GLN
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  251 SER
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 121 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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  64 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 = 0.4282 r_free = 0.4282 target = 0.135336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.112456 restraints weight = 33853.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.111832 restraints weight = 55689.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.112482 restraints weight = 50891.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.113988 restraints weight = 32492.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.114103 restraints weight = 22280.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.2921

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= 0.145
  Angle     :  0.570  11.814  15535  Z= 0.285
  Chirality :  0.041   0.192   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  3.990  20.096   1606
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.10 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.22), residues: 1455
  helix:  1.68 (0.18), residues: 787
  sheet: -0.61 (0.43), residues: 155
  loop : -0.45 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 370 
 TYR   0.021   0.001   TYR B 205 
 PHE   0.017   0.001   PHE C 191 
 TRP   0.019   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11483)
  covalent geometry    : angle       0.57020 (15535)
  hydrogen bonds       : bond        0.03430 (  642)
  hydrogen bonds       : angle       4.07629 ( 1884)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1509.90 seconds
wall clock time: 26 minutes 59.02 seconds (1619.02 seconds total)