Starting phenix.real_space_refine
on Wed May 14 02:51:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxf_40850/05_2025/8sxf_40850.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxf_40850/05_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_40850/05_2025/8sxf_40850.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxf_40850/05_2025/8sxf_40850.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxf_40850/05_2025/8sxf_40850.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxf_40850/05_2025/8sxf_40850.cif"
  }
  resolution = 3.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    7074      2.51       5
     N    2013      2.21       5
     O    2217      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11321
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2733
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 20, 'TRANS': 343}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2707
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 20, 'TRANS': 340}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4248
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 512}
    Chain: "D"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 30
          Classifications: {'peptide': 6}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'TRANS': 5}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'UNK:plan-1': 6}
          Unresolved non-hydrogen planarities: 6
    Chain: "E"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1603
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 10, 'TRANS': 203}
          Chain breaks: 2
  Time building chain proxies: 7.12, per 1000 atoms: 0.63
  Number of scatterers: 11321
  At special positions: 0
  Unit cell: (91.908, 132.894, 182.574, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O    2217      8.00
     N    2013      7.00
     C    7074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 14 sheets defined
      56.2% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 60
    Processing helix  chain 'A' and resid 65 through 82
      removed outlier: 4.086A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 101
    Processing helix  chain 'A' and resid 127 through 132
      removed outlier: 3.814A  pdb=" N   ARG A 131 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 161
    Processing helix  chain 'A' and resid 214 through 230
    Processing helix  chain 'A' and resid 248 through 259
      removed outlier: 3.519A  pdb=" N   ALA A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 314
      removed outlier: 3.577A  pdb=" N   VAL A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.793A  pdb=" N   ARG A 340 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 417
      removed outlier: 4.231A  pdb=" N   SER A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 435
    Processing helix  chain 'B' and resid 42 through 59
    Processing helix  chain 'B' and resid 65 through 80
      removed outlier: 3.548A  pdb=" N   LEU B  69 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 98
      removed outlier: 3.548A  pdb=" N   GLU B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 132
    Processing helix  chain 'B' and resid 152 through 161
    Processing helix  chain 'B' and resid 214 through 231
    Processing helix  chain 'B' and resid 248 through 260
    Processing helix  chain 'B' and resid 272 through 276
      removed outlier: 3.601A  pdb=" N   GLU B 276 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 314
    Processing helix  chain 'B' and resid 412 through 417
      removed outlier: 4.063A  pdb=" N   ASP B 417 " --> pdb=" O   PRO B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 435
    Processing helix  chain 'C' and resid 49 through 65
    Processing helix  chain 'C' and resid 67 through 83
      removed outlier: 3.535A  pdb=" N   ALA C  71 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 99
    Processing helix  chain 'C' and resid 100 through 115
    Processing helix  chain 'C' and resid 118 through 132
      removed outlier: 3.641A  pdb=" N   GLN C 122 " --> pdb=" O   ASN C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 148
    Processing helix  chain 'C' and resid 153 through 164
      removed outlier: 4.263A  pdb=" N   LEU C 157 " --> pdb=" O   HIS C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 183
    Processing helix  chain 'C' and resid 187 through 201
    Processing helix  chain 'C' and resid 203 through 213
      removed outlier: 3.556A  pdb=" N   ASN C 213 " --> pdb=" O   LEU C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 219
    Processing helix  chain 'C' and resid 220 through 234
    Processing helix  chain 'C' and resid 235 through 250
      removed outlier: 3.611A  pdb=" N   ALA C 239 " --> pdb=" O   ARG C 235 " (cutoff:3.500A)
      Proline residue:  C 241  - end of helix
    Processing helix  chain 'C' and resid 253 through 268
      removed outlier: 4.377A  pdb=" N   ARG C 257 " --> pdb=" O   ASP C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 284
    Processing helix  chain 'C' and resid 287 through 301
    Processing helix  chain 'C' and resid 303 through 318
    Processing helix  chain 'C' and resid 320 through 336
    Processing helix  chain 'C' and resid 337 through 348
      removed outlier: 3.503A  pdb=" N   TYR C 345 " --> pdb=" O   ALA C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 353 through 368
    Processing helix  chain 'C' and resid 370 through 385
      removed outlier: 3.874A  pdb=" N   GLN C 385 " --> pdb=" O   ALA C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 404
      removed outlier: 3.903A  pdb=" N   GLN C 391 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 420
    Processing helix  chain 'C' and resid 423 through 438
    Processing helix  chain 'C' and resid 439 through 454
      removed outlier: 4.626A  pdb=" N   MET C 443 " --> pdb=" O   ASP C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 472
    Processing helix  chain 'C' and resid 475 through 489
    Processing helix  chain 'C' and resid 492 through 507
      removed outlier: 3.544A  pdb=" N   LEU C 496 " --> pdb=" O   ASP C 492 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 509 through 523
    Processing helix  chain 'C' and resid 525 through 540
    Processing helix  chain 'C' and resid 541 through 556
      removed outlier: 4.211A  pdb=" N   ALA C 545 " --> pdb=" O   ARG C 541 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR C 552 " --> pdb=" O   ILE C 548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 570
    Processing helix  chain 'E' and resid 214 through 230
      removed outlier: 4.002A  pdb=" N   GLU E 218 " --> pdb=" O   ASN E 214 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 260
    Processing helix  chain 'E' and resid 302 through 314
    Processing helix  chain 'E' and resid 412 through 417
    Processing helix  chain 'E' and resid 417 through 434
    Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106
    Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 114
      removed outlier: 6.632A  pdb=" N   GLY A 112 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   VAL A 120 " --> pdb=" O   GLY A 112 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLU A 114 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   ILE A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147
      removed outlier: 5.145A  pdb=" N   ILE A 140 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 200
      removed outlier: 5.459A  pdb=" N   SER A 196 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   VAL A 198 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   TYR A 205 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ALA A 204 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ASP A 240 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU A 206 " --> pdb=" O   ASP A 240 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU A 292 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   MET A 320 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL A 294 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280
      removed outlier: 3.759A  pdb=" N   TYR A 267 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL A 330 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374
    Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 88
      removed outlier: 3.505A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88
      removed outlier: 3.505A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ARG B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL B 330 " --> pdb=" O   THR B 346 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.859A  pdb=" N   GLY B 162 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 114
      removed outlier: 6.891A  pdb=" N   GLU B 110 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 143
    Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 170
    Processing sheet with id=AB4, first strand: chain 'B' and resid 194 through 200
      removed outlier: 5.132A  pdb=" N   SER B 196 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG B 207 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   VAL B 198 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   TYR B 205 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU B 200 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 204 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP B 240 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 208 " --> pdb=" O   ASP B 240 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL B 293 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 8.848A  pdb=" N   MET B 320 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL B 294 " --> pdb=" O   MET B 320 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 198
      removed outlier: 3.836A  pdb=" N   ILE E 208 " --> pdb=" O   ASP E 240 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU E 237 " --> pdb=" O   VAL E 293 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   LEU E 295 " --> pdb=" O   LEU E 237 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   LEU E 239 " --> pdb=" O   LEU E 295 " (cutoff:3.500A)

    645 hydrogen bonds defined for protein.
    1884 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.39

  Time building geometry restraints manager: 3.41 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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     27.820
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.0000

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

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.22), residues: 1455
  helix:  2.04 (0.19), residues: 754
  sheet: -0.54 (0.42), residues: 161
  loop : -0.43 (0.27), residues: 540

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

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

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.247 
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: 0.2618
  time to fit residues: 42.6949
Evaluate side-chains
  68 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    0.0170
   chunk 110 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   chunk 37 optimal weight:    0.3980
   chunk 74 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 114 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 69 optimal weight:    0.2980
   chunk 85 optimal weight:    0.9990
   chunk 132 optimal weight:    0.4980
   overall best weight:    0.2596

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.136794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.113425 restraints weight = 33138.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.112186 restraints weight = 46920.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.113410 restraints weight = 42853.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1558

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

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

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

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

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

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  259 PHE cc_start: 0.6648 (m-80) cc_final: 0.6162 (m-10)
REVERT: C  376 GLN cc_start: 0.7036 (pp30) cc_final: 0.6710 (pp30)
REVERT: E  214 ASN cc_start: 0.8153 (m-40) cc_final: 0.7890 (t0)
REVERT: E  226 LEU cc_start: 0.7187 (tp) cc_final: 0.6909 (tt)
REVERT: E  233 ARG cc_start: 0.6094 (tpm170) cc_final: 0.5834 (mmm160)
REVERT: E  385 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6596 (mm-30)
  outliers start: 20
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2558
  time to fit residues: 36.2918
Evaluate side-chains
  79 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  249 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0970
   chunk 107 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 142 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 127 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.135835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.112688 restraints weight = 33834.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.111895 restraints weight = 52634.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.113250 restraints weight = 44931.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
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   0.028  11483  Z= 0.135
  Angle     :  0.562   7.571  15535  Z= 0.281
  Chirality :  0.040   0.147   1763
  Planarity :  0.004   0.051   2074
  Dihedral  :  4.031  19.618   1606
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.32 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.22), residues: 1455
  helix:  1.78 (0.18), residues: 783
  sheet: -0.66 (0.41), residues: 171
  loop : -0.25 (0.27), residues: 501

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  642)
  hydrogen bonds       : angle       4.26947 ( 1884)
  covalent geometry    : bond        0.00304 (11483)
  covalent geometry    : angle       0.56193 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8124 (tt)
REVERT: B   77 MET cc_start: 0.8358 (ttp) cc_final: 0.7860 (ptt)
REVERT: C  376 GLN cc_start: 0.6995 (pp30) cc_final: 0.6727 (pp30)
REVERT: E  214 ASN cc_start: 0.8189 (m-40) cc_final: 0.7926 (t0)
REVERT: E  381 GLU cc_start: 0.7501 (tp30) cc_final: 0.7274 (tp30)
REVERT: E  385 GLU cc_start: 0.7744 (mm-30) cc_final: 0.6743 (mm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2198
  time to fit residues: 32.8478
Evaluate side-chains
  78 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 129 optimal weight:    0.1980
   chunk 91 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B  84 HIS
E 212 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.136626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.114410 restraints weight = 33632.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.114078 restraints weight = 58932.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.114697 restraints weight = 50235.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11483  Z= 0.190
  Angle     :  0.608  12.760  15535  Z= 0.302
  Chirality :  0.041   0.149   1763
  Planarity :  0.004   0.053   2074
  Dihedral  :  4.219  21.528   1606
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.83 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.22), residues: 1455
  helix:  1.66 (0.18), residues: 783
  sheet: -0.56 (0.43), residues: 159
  loop : -0.39 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.011   0.001   PHE A 325 
 TYR   0.023   0.002   TYR B 205 
 ARG   0.003   0.000   ARG E 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03817 (  642)
  hydrogen bonds       : angle       4.29351 ( 1884)
  covalent geometry    : bond        0.00440 (11483)
  covalent geometry    : angle       0.60758 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 1.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8329 (tt)
REVERT: A  199 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7610 (mp)
REVERT: B   77 MET cc_start: 0.8402 (ttp) cc_final: 0.8046 (ptt)
REVERT: C  376 GLN cc_start: 0.7051 (pp30) cc_final: 0.6783 (pp30)
REVERT: E  212 GLN cc_start: 0.5606 (OUTLIER) cc_final: 0.5261 (pp30)
REVERT: E  385 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7135 (mm-30)
  outliers start: 28
  outliers final: 17
  residues processed: 96
  average time/residue: 0.2341
  time to fit residues: 33.0131
Evaluate side-chains
  86 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  349 TYR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  212 GLN
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 99 optimal weight:    9.9990
   chunk 119 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.131092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.106986 restraints weight = 33363.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.108405 restraints weight = 50381.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.108427 restraints weight = 36342.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11483  Z= 0.230
  Angle     :  0.645  12.449  15535  Z= 0.320
  Chirality :  0.042   0.181   1763
  Planarity :  0.004   0.057   2074
  Dihedral  :  4.394  23.340   1606
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.59 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.22), residues: 1455
  helix:  1.48 (0.18), residues: 784
  sheet: -0.62 (0.43), residues: 159
  loop : -0.51 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 501 
 HIS   0.004   0.001   HIS C 526 
 PHE   0.025   0.002   PHE E 325 
 TYR   0.024   0.002   TYR B 205 
 ARG   0.003   0.000   ARG E 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  642)
  hydrogen bonds       : angle       4.39727 ( 1884)
  covalent geometry    : bond        0.00532 (11483)
  covalent geometry    : angle       0.64498 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 73
  time to evaluate  : 1.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8023 (tt)
REVERT: A  199 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7542 (mp)
REVERT: C  139 MET cc_start: 0.6948 (ttt) cc_final: 0.6536 (tmm)
REVERT: C  376 GLN cc_start: 0.7101 (pp30) cc_final: 0.6766 (pp30)
REVERT: C  406 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5315 (mm-40)
REVERT: E  385 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7028 (mm-30)
  outliers start: 34
  outliers final: 19
  residues processed: 104
  average time/residue: 0.2197
  time to fit residues: 34.5397
Evaluate side-chains
  91 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
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  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  349 TYR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain 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  366 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 128 optimal weight:    0.0980
   chunk 54 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 138 optimal weight:    0.6980
   chunk 124 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.135265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.112124 restraints weight = 33755.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.111282 restraints weight = 47934.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.112435 restraints weight = 43285.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.2394

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= 0.123
  Angle     :  0.557  13.435  15535  Z= 0.278
  Chirality :  0.040   0.147   1763
  Planarity :  0.004   0.055   2074
  Dihedral  :  4.076  20.277   1606
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.22), residues: 1455
  helix:  1.67 (0.18), residues: 784
  sheet: -0.71 (0.41), residues: 171
  loop : -0.37 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 501 
 HIS   0.007   0.001   HIS C 526 
 PHE   0.016   0.001   PHE C 191 
 TYR   0.019   0.001   TYR B 205 
 ARG   0.007   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  642)
  hydrogen bonds       : angle       4.15621 ( 1884)
  covalent geometry    : bond        0.00277 (11483)
  covalent geometry    : angle       0.55745 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8307 (tt)
REVERT: A  199 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7535 (mp)
REVERT: B   77 MET cc_start: 0.8178 (ttp) cc_final: 0.7688 (ptt)
REVERT: C  376 GLN cc_start: 0.7130 (pp30) cc_final: 0.6816 (pp30)
REVERT: E  385 GLU cc_start: 0.7994 (mm-30) cc_final: 0.6928 (mm-30)
  outliers start: 31
  outliers final: 16
  residues processed: 112
  average time/residue: 0.2300
  time to fit residues: 38.0821
Evaluate side-chains
  88 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0470
   chunk 133 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 123 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0170
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
C 231 GLN
C 302 GLN
C 438 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.135781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.112120 restraints weight = 33668.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.110884 restraints weight = 48449.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.112093 restraints weight = 41458.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2659

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= 0.123
  Angle     :  0.573  13.894  15535  Z= 0.285
  Chirality :  0.040   0.180   1763
  Planarity :  0.004   0.054   2074
  Dihedral  :  4.005  19.428   1606
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.43 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.22), residues: 1455
  helix:  1.72 (0.18), residues: 785
  sheet: -0.69 (0.42), residues: 157
  loop : -0.45 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 501 
 HIS   0.006   0.001   HIS C 526 
 PHE   0.021   0.001   PHE C 191 
 TYR   0.021   0.001   TYR B 418 
 ARG   0.005   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  642)
  hydrogen bonds       : angle       4.05213 ( 1884)
  covalent geometry    : bond        0.00277 (11483)
  covalent geometry    : angle       0.57335 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8264 (tt)
REVERT: B   77 MET cc_start: 0.8177 (ttp) cc_final: 0.7781 (ptt)
REVERT: B  259 PHE cc_start: 0.6688 (m-80) cc_final: 0.6126 (m-80)
REVERT: C  376 GLN cc_start: 0.7151 (pp30) cc_final: 0.6808 (pp30)
REVERT: E  385 GLU cc_start: 0.7835 (mm-30) cc_final: 0.6876 (mm-30)
  outliers start: 34
  outliers final: 22
  residues processed: 105
  average time/residue: 0.2393
  time to fit residues: 36.9506
Evaluate side-chains
  95 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  231 GLN
Chi-restraints excluded: chain C residue  459 MET
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0050
   chunk 90 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    9.9990
   chunk 78 optimal weight:    0.7980
   chunk 109 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0970
   chunk 125 optimal weight:    0.2980
   overall best weight:    0.3992

-------------------------------------------------------------------------------
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 231 GLN
C 438 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.136554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.113569 restraints weight = 33720.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.112791 restraints weight = 50402.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.113512 restraints weight = 46584.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.2771

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= 0.114
  Angle     :  0.573  14.141  15535  Z= 0.284
  Chirality :  0.041   0.195   1763
  Planarity :  0.004   0.054   2074
  Dihedral  :  3.934  18.478   1606
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.18 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.22), residues: 1455
  helix:  1.77 (0.18), residues: 784
  sheet: -0.60 (0.43), residues: 149
  loop : -0.46 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.024   0.001   PHE C 191 
 TYR   0.016   0.001   TYR B 205 
 ARG   0.007   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03296 (  642)
  hydrogen bonds       : angle       4.03240 ( 1884)
  covalent geometry    : bond        0.00255 (11483)
  covalent geometry    : angle       0.57254 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8311 (tt)
REVERT: B   77 MET cc_start: 0.8183 (ttp) cc_final: 0.7836 (ptt)
REVERT: B  259 PHE cc_start: 0.6510 (m-80) cc_final: 0.5966 (m-80)
REVERT: C  376 GLN cc_start: 0.7131 (pp30) cc_final: 0.6926 (pp30)
REVERT: E  377 ARG cc_start: 0.6209 (mmp80) cc_final: 0.5797 (mmp80)
REVERT: E  385 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6847 (mm-30)
  outliers start: 26
  outliers final: 23
  residues processed: 95
  average time/residue: 0.2395
  time to fit residues: 34.0627
Evaluate side-chains
  96 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  231 GLN
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  459 MET
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 145 optimal weight:    0.9980
   chunk 100 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 42 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.135397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.113691 restraints weight = 33991.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.113457 restraints weight = 54541.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.114053 restraints weight = 48906.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2836

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= 0.127
  Angle     :  0.568  14.138  15535  Z= 0.281
  Chirality :  0.040   0.171   1763
  Planarity :  0.004   0.053   2074
  Dihedral  :  3.927  18.860   1606
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.01 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.22), residues: 1455
  helix:  1.77 (0.18), residues: 785
  sheet: -0.71 (0.41), residues: 164
  loop : -0.38 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.022   0.001   PHE C 191 
 TYR   0.026   0.001   TYR B 418 
 ARG   0.006   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  642)
  hydrogen bonds       : angle       4.04861 ( 1884)
  covalent geometry    : bond        0.00292 (11483)
  covalent geometry    : angle       0.56803 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 68
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8228 (tt)
REVERT: B  259 PHE cc_start: 0.6627 (m-80) cc_final: 0.6099 (m-80)
REVERT: C  139 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5340 (tmm)
REVERT: E  385 GLU cc_start: 0.7820 (mm-30) cc_final: 0.6888 (mm-30)
  outliers start: 31
  outliers final: 22
  residues processed: 93
  average time/residue: 0.2107
  time to fit residues: 29.7610
Evaluate side-chains
  91 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
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  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  139 MET
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  231 GLN
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 125 optimal weight:    0.4980
   chunk 56 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.139041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.116669 restraints weight = 33862.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.116236 restraints weight = 57015.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.116949 restraints weight = 49222.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.2877

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= 0.129
  Angle     :  0.585  15.053  15535  Z= 0.288
  Chirality :  0.041   0.196   1763
  Planarity :  0.004   0.053   2074
  Dihedral  :  3.933  18.693   1606
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.77 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.22), residues: 1455
  helix:  1.70 (0.18), residues: 785
  sheet: -0.70 (0.41), residues: 164
  loop : -0.35 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.021   0.001   PHE C 191 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.006   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  642)
  hydrogen bonds       : angle       4.06187 ( 1884)
  covalent geometry    : bond        0.00295 (11483)
  covalent geometry    : angle       0.58503 (15535)

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

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8347 (tt)
REVERT: B  259 PHE cc_start: 0.6636 (m-80) cc_final: 0.6067 (m-80)
REVERT: C  139 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5503 (tmm)
REVERT: E  385 GLU cc_start: 0.7869 (mm-30) cc_final: 0.6877 (mm-30)
  outliers start: 25
  outliers final: 22
  residues processed: 88
  average time/residue: 0.2107
  time to fit residues: 28.3783
Evaluate side-chains
  90 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
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  306 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain C residue   75 TYR
Chi-restraints excluded: chain C residue  139 MET
Chi-restraints excluded: chain C residue  153 HIS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Chi-restraints excluded: chain C residue  255 ARG
Chi-restraints excluded: chain C residue  459 MET
Chi-restraints excluded: chain C residue  480 GLU
Chi-restraints excluded: chain E residue  238 VAL
Chi-restraints excluded: chain E residue  248 VAL
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 ILE
Chi-restraints excluded: chain E residue  366 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 120 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.1786

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.137361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.114870 restraints weight = 33772.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.114269 restraints weight = 56969.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.114948 restraints weight = 52077.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11483  Z= 0.176
  Angle     :  0.617  14.447  15535  Z= 0.305
  Chirality :  0.041   0.189   1763
  Planarity :  0.004   0.055   2074
  Dihedral  :  4.130  21.118   1606
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.68 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.22), residues: 1455
  helix:  1.54 (0.18), residues: 786
  sheet: -0.73 (0.42), residues: 157
  loop : -0.44 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 501 
 HIS   0.005   0.001   HIS C 526 
 PHE   0.018   0.001   PHE C 191 
 TYR   0.023   0.002   TYR B 418 
 ARG   0.006   0.000   ARG E 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  642)
  hydrogen bonds       : angle       4.19419 ( 1884)
  covalent geometry    : bond        0.00408 (11483)
  covalent geometry    : angle       0.61654 (15535)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3093.35 seconds
wall clock time: 55 minutes 18.84 seconds (3318.84 seconds total)