Starting phenix.real_space_refine
on Wed Mar 12 19:44:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uph_42448/03_2025/8uph_42448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uph_42448/03_2025/8uph_42448.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uph_42448/03_2025/8uph_42448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uph_42448/03_2025/8uph_42448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uph_42448/03_2025/8uph_42448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uph_42448/03_2025/8uph_42448.cif"
  }
  resolution = 4.13
  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=   0.007
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      19      5.16       5
     C    5140      2.51       5
     N    1473      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8121
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4101
          Classifications: {'peptide': 538}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 501}
    Chain: "B"
      Number of atoms: 3934
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 516, 3924
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480}
      Conformer: "B"
        Number of residues, atoms: 516, 3924
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480}
          bond proxies already assigned to first conformer: 3997
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'BLA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'BLA': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS B 315 " occ=0.52
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 315 " occ=0.48
  Time building chain proxies: 7.71, per 1000 atoms: 0.95
  Number of scatterers: 8121
  At special positions: 0
  Unit cell: (81.024, 116.472, 163.736, 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      19     16.00
     O    1489      8.00
     N    1473      7.00
     C    5140      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 11 sheets defined
      45.6% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
      removed outlier: 3.584A  pdb=" N   ARG A  15 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 54 through 59
      removed outlier: 3.909A  pdb=" N   LEU A  58 " --> pdb=" O   PRO A  54 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU A  59 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 54 through 59'
    Processing helix  chain 'A' and resid 62 through 67
      removed outlier: 3.600A  pdb=" N   VAL A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 74
      removed outlier: 3.961A  pdb=" N   GLN A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 82
      removed outlier: 3.580A  pdb=" N   LEU A  78 " --> pdb=" O   GLN A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 130
      removed outlier: 4.099A  pdb=" N   THR A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 154
    Processing helix  chain 'A' and resid 189 through 193
    Processing helix  chain 'A' and resid 194 through 202
    Processing helix  chain 'A' and resid 242 through 253
      removed outlier: 3.603A  pdb=" N   MET A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 330
      removed outlier: 3.888A  pdb=" N   VAL A 292 " --> pdb=" O   ARG A 288 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   THR A 294 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLN A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
      Proline residue:  A 322  - end of helix
      removed outlier: 3.637A  pdb=" N   GLY A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 340
    Processing helix  chain 'A' and resid 340 through 346
      removed outlier: 3.716A  pdb=" N   VAL A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 340 through 346'
    Processing helix  chain 'A' and resid 369 through 381
    Processing helix  chain 'A' and resid 399 through 403
      removed outlier: 4.079A  pdb=" N   ALA A 403 " --> pdb=" O   PRO A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 546
      removed outlier: 3.900A  pdb=" N   LEU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   GLY A 491 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      Proline residue:  A 528  - end of helix
      removed outlier: 3.831A  pdb=" N   MET A 540 " --> pdb=" O   ALA A 536 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   GLU A 541 " --> pdb=" O   GLY A 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 16
      removed outlier: 3.536A  pdb=" N   GLU B  16 " --> pdb=" O   GLN B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 3.897A  pdb=" N   LEU B  21 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLY B  22 " --> pdb=" O   HIS B  19 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 18 through 22'
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 55 through 59
    Processing helix  chain 'B' and resid 62 through 66
      removed outlier: 3.792A  pdb=" N   GLN B  65 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL B  66 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 62 through 66'
    Processing helix  chain 'B' and resid 74 through 82
    Processing helix  chain 'B' and resid 116 through 130
      removed outlier: 4.009A  pdb=" N   THR B 120 " --> pdb=" O   ASP B 116 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA B 121 " --> pdb=" O   MET B 117 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU B 122 " --> pdb=" O   GLU B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 154
      removed outlier: 3.583A  pdb=" N   LEU B 141 " --> pdb=" O   GLY B 137 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN B 143 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   THR B 148 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 193
    Processing helix  chain 'B' and resid 194 through 204
      removed outlier: 3.863A  pdb=" N   ARG B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 253
      removed outlier: 3.723A  pdb=" N   LEU B 246 " --> pdb=" O   SER B 242 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU B 247 " --> pdb=" O   PRO B 243 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR B 248 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 327
      removed outlier: 3.789A  pdb=" N   LEU B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ALA B 298 " --> pdb=" O   THR B 294 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU B 299 " --> pdb=" O   GLN B 295 " (cutoff:3.500A)
      Proline residue:  B 322  - end of helix
    Processing helix  chain 'B' and resid 332 through 340
    Processing helix  chain 'B' and resid 344 through 348
      removed outlier: 3.535A  pdb=" N   LEU B 347 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 380
      removed outlier: 3.539A  pdb=" N   VAL B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   GLU B 374 " --> pdb=" O   MET B 370 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ALA B 375 " --> pdb=" O   ASP B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 398
      removed outlier: 4.596A  pdb=" N   LEU B 397 " --> pdb=" O   ARG B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 403
      removed outlier: 3.988A  pdb=" N   ALA B 402 " --> pdb=" O   TYR B 398 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ALA B 403 " --> pdb=" O   PRO B 399 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 398 through 403'
    Processing helix  chain 'B' and resid 476 through 524
      removed outlier: 3.549A  pdb=" N   ALA B 480 " --> pdb=" O   ARG B 476 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLU B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   GLY B 491 " --> pdb=" O   SER B 487 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL B 492 " --> pdb=" O   ALA B 488 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   LEU B 494 " --> pdb=" O   ILE B 490 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24
      removed outlier: 3.658A  pdb=" N   VAL A 220 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A  43 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLU A  41 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ALA A  32 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   VAL A  43 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.645A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 365
      removed outlier: 3.650A  pdb=" N   LEU A 425 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 412 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR A 391 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 438
      removed outlier: 4.409A  pdb=" N   ARG A 433 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A 467 " --> pdb=" O   ARG A 433 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A 435 " --> pdb=" O   GLU A 465 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU A 465 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 447
    Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33
      removed outlier: 3.502A  pdb=" N   VAL B  29 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL B 105 " --> pdb=" O   HIS B  98 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   HIS B  98 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLU B 107 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B  96 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 188
      removed outlier: 5.786A  pdb=" N   VAL B 171 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ARG B 162 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ALA B 173 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B 157 " --> pdb=" O   HIS B 275 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   TRP B 269 " --> pdb=" O   PHE B 163 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LYS B 264 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY B 270 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER B 259 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 362 through 365
      removed outlier: 3.757A  pdb=" N   GLY B 352 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B 410 " --> pdb=" O   ARG B 428 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 438
      removed outlier: 3.848A  pdb=" N   ARG B 433 " --> pdb=" O   VAL B 467 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 446 through 447

    405 hydrogen bonds defined for protein.
    1135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1515
        1.32 -     1.44: 1985
        1.44 -     1.56: 4772
        1.56 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 8304
  Sorted by residual:
  bond pdb=" C1D BLA A 801 "
       pdb=" CHD BLA A 801 "
    ideal  model  delta    sigma   weight residual
    1.440  1.339  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C1D BLA B 801 "
       pdb=" CHD BLA B 801 "
    ideal  model  delta    sigma   weight residual
    1.440  1.339  0.101 2.00e-02 2.50e+03 2.53e+01
  bond pdb=" C3C BLA A 801 "
       pdb=" CAC BLA A 801 "
    ideal  model  delta    sigma   weight residual
    1.458  1.360  0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" C3C BLA A 801 "
       pdb=" C4C BLA A 801 "
    ideal  model  delta    sigma   weight residual
    1.471  1.375  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" C3C BLA B 801 "
       pdb=" C4C BLA B 801 "
    ideal  model  delta    sigma   weight residual
    1.471  1.389  0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 8299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 10987
        1.90 -     3.79: 280
        3.79 -     5.69: 34
        5.69 -     7.58: 14
        7.58 -     9.48: 4
  Bond angle restraints: 11319
  Sorted by residual:
  angle pdb=" CA  ARG B 502 "
        pdb=" CB  ARG B 502 "
        pdb=" CG  ARG B 502 "
      ideal   model   delta    sigma   weight residual
     114.10  123.58   -9.48 2.00e+00 2.50e-01 2.25e+01
  angle pdb=" C   GLU B 501 "
        pdb=" N   ARG B 502 "
        pdb=" CA  ARG B 502 "
      ideal   model   delta    sigma   weight residual
     121.58  114.87    6.71 1.95e+00 2.63e-01 1.18e+01
  angle pdb=" C1C BLA A 801 "
        pdb=" C2C BLA A 801 "
        pdb=" CMC BLA A 801 "
      ideal   model   delta    sigma   weight residual
     121.37  130.29   -8.92 3.00e+00 1.11e-01 8.85e+00
  angle pdb=" C   GLY A 518 "
        pdb=" N   HIS A 519 "
        pdb=" CA  HIS A 519 "
      ideal   model   delta    sigma   weight residual
     121.58  116.26    5.32 1.95e+00 2.63e-01 7.43e+00
  angle pdb=" C   GLN B  65 "
        pdb=" N   VAL B  66 "
        pdb=" CA  VAL B  66 "
      ideal   model   delta    sigma   weight residual
     122.66  120.10    2.56 9.70e-01 1.06e+00 6.96e+00
  ... (remaining 11314 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 4525
       17.42 -    34.85: 411
       34.85 -    52.27: 73
       52.27 -    69.69: 12
       69.69 -    87.11: 11
  Dihedral angle restraints: 5032
    sinusoidal: 2014
      harmonic: 3018
  Sorted by residual:
  dihedral pdb=" CA  ARG B 502 "
           pdb=" C   ARG B 502 "
           pdb=" N   LEU B 503 "
           pdb=" CA  LEU B 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.89   27.11     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  LYS A 475 "
           pdb=" C   LYS A 475 "
           pdb=" N   ARG A 476 "
           pdb=" CA  ARG A 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.41  -24.59     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  LEU B 489 "
           pdb=" C   LEU B 489 "
           pdb=" N   ILE B 490 "
           pdb=" CA  ILE B 490 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.01   20.99     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 5029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1032
       0.050 -    0.100: 192
       0.100 -    0.150: 43
       0.150 -    0.200: 0
       0.200 -    0.250: 1
  Chirality restraints: 1268
  Sorted by residual:
  chirality pdb=" CA  ARG B 502 "
            pdb=" N   ARG B 502 "
            pdb=" C   ARG B 502 "
            pdb=" CB  ARG B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  ASP B 265 "
            pdb=" N   ASP B 265 "
            pdb=" C   ASP B 265 "
            pdb=" CB  ASP B 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CB  ILE A 490 "
            pdb=" CA  ILE A 490 "
            pdb=" CG1 ILE A 490 "
            pdb=" CG2 ILE A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1265 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA A 801 "   -0.127 2.00e-02 2.50e+03   4.54e-01 5.14e+03
        pdb=" C1D BLA A 801 "    0.011 2.00e-02 2.50e+03
        pdb=" C2C BLA A 801 "    0.163 2.00e-02 2.50e+03
        pdb=" C3C BLA A 801 "   -0.237 2.00e-02 2.50e+03
        pdb=" C4C BLA A 801 "    0.119 2.00e-02 2.50e+03
        pdb=" CAC BLA A 801 "   -0.880 2.00e-02 2.50e+03
        pdb=" CHD BLA A 801 "    0.602 2.00e-02 2.50e+03
        pdb=" CMC BLA A 801 "    0.809 2.00e-02 2.50e+03
        pdb=" NC  BLA A 801 "   -0.075 2.00e-02 2.50e+03
        pdb=" OC  BLA A 801 "   -0.385 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA B 801 "   -0.130 2.00e-02 2.50e+03   3.68e-01 3.39e+03
        pdb=" C1D BLA B 801 "    0.123 2.00e-02 2.50e+03
        pdb=" C2C BLA B 801 "    0.131 2.00e-02 2.50e+03
        pdb=" C3C BLA B 801 "   -0.183 2.00e-02 2.50e+03
        pdb=" C4C BLA B 801 "    0.036 2.00e-02 2.50e+03
        pdb=" CAC BLA B 801 "   -0.663 2.00e-02 2.50e+03
        pdb=" CHD BLA B 801 "    0.513 2.00e-02 2.50e+03
        pdb=" CMC BLA B 801 "    0.663 2.00e-02 2.50e+03
        pdb=" NC  BLA B 801 "   -0.310 2.00e-02 2.50e+03
        pdb=" OC  BLA B 801 "   -0.179 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  BLA A 801 "   -0.281 2.00e-02 2.50e+03   3.34e-01 2.79e+03
        pdb=" OB  BLA A 801 "   -0.172 2.00e-02 2.50e+03
        pdb=" C1B BLA A 801 "   -0.168 2.00e-02 2.50e+03
        pdb=" C2B BLA A 801 "   -0.149 2.00e-02 2.50e+03
        pdb=" C3B BLA A 801 "    0.167 2.00e-02 2.50e+03
        pdb=" C4A BLA A 801 "    0.567 2.00e-02 2.50e+03
        pdb=" C4B BLA A 801 "   -0.103 2.00e-02 2.50e+03
        pdb=" CAB BLA A 801 "    0.645 2.00e-02 2.50e+03
        pdb=" CHB BLA A 801 "   -0.090 2.00e-02 2.50e+03
        pdb=" CMB BLA A 801 "   -0.415 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1476
        2.77 -     3.30: 8226
        3.30 -     3.83: 13593
        3.83 -     4.37: 14603
        4.37 -     4.90: 24498
  Nonbonded interactions: 62396
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 127 "
            pdb=" OG  SER A 130 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   GLY A 330 "
            pdb=" NH1 ARG A 495 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   GLU B 505 "
            pdb=" OG  SER B 508 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ALA A 516 "
            pdb=" OG1 THR A 520 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   PHE B 385 "
            pdb=" NH1 ARG B 415 "
     model   vdw
     2.274 3.120
  ... (remaining 62391 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 9 through 314 or resid 316 through 524 or resid 801))
  selection = (chain 'B' and (resid 9 through 314 or resid 316 through 524 or resid 801))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 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:             4.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.850
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
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      :  0.004   0.101   8304  Z= 0.286
  Angle     :  0.714   9.477  11319  Z= 0.352
  Chirality :  0.040   0.250   1268
  Planarity :  0.021   0.454   1488
  Dihedral  : 14.178  87.112   3084
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.29 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.37 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -0.18 (0.25), residues: 1053
  helix:  0.39 (0.26), residues: 393
  sheet:  0.35 (0.38), residues: 170
  loop : -0.62 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B  72 
 HIS   0.015   0.001   HIS B 519 
 PHE   0.020   0.001   PHE B 517 
 TYR   0.013   0.001   TYR B  27 
 ARG   0.006   0.000   ARG A 530 

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

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

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A  345 LEU cc_start: 0.9388 (mt) cc_final: 0.9114 (mt)
REVERT: A  362 LEU cc_start: 0.9222 (tp) cc_final: 0.8897 (tt)
REVERT: B  252 MET cc_start: 0.9233 (tpp) cc_final: 0.8682 (tpp)
REVERT: B  290 CYS cc_start: 0.9408 (m) cc_final: 0.9135 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 64
  average time/residue: 0.2235
  time to fit residues: 19.6427
Evaluate side-chains
  50 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.058530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.037150 restraints weight = 123390.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.038956 restraints weight = 48773.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.040243 restraints weight = 29471.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8304  Z= 0.257
  Angle     :  0.682   9.772  11319  Z= 0.339
  Chirality :  0.041   0.169   1268
  Planarity :  0.006   0.049   1488
  Dihedral  :  6.765  76.230   1215
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -0.24 (0.25), residues: 1053
  helix:  0.54 (0.26), residues: 394
  sheet:  0.06 (0.37), residues: 192
  loop : -0.78 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  72 
 HIS   0.015   0.002   HIS B 519 
 PHE   0.018   0.002   PHE B 517 
 TYR   0.012   0.002   TYR B 161 
 ARG   0.005   0.001   ARG B  94 

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

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

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 MET cc_start: 0.8952 (mmm) cc_final: 0.8720 (mmm)
REVERT: A  284 TYR cc_start: 0.8902 (t80) cc_final: 0.8648 (t80)
REVERT: A  345 LEU cc_start: 0.9428 (mt) cc_final: 0.9090 (mt)
REVERT: A  362 LEU cc_start: 0.9155 (tp) cc_final: 0.8796 (tt)
REVERT: B  180 MET cc_start: 0.7833 (ptp) cc_final: 0.7451 (mpp)
REVERT: B  290 CYS cc_start: 0.9508 (m) cc_final: 0.9253 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2316
  time to fit residues: 17.4214
Evaluate side-chains
  42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 86 optimal weight:    0.4980
   chunk 76 optimal weight:    0.0030
   chunk 48 optimal weight:    0.9980
   chunk 103 optimal weight:   20.0000
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
B  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.059628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.038345 restraints weight = 111823.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.040136 restraints weight = 44257.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.041401 restraints weight = 26839.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8304  Z= 0.162
  Angle     :  0.634   9.576  11319  Z= 0.312
  Chirality :  0.040   0.155   1268
  Planarity :  0.005   0.048   1488
  Dihedral  :  6.545  77.123   1215
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.32 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -0.19 (0.25), residues: 1053
  helix:  0.60 (0.26), residues: 387
  sheet:  0.26 (0.37), residues: 185
  loop : -0.83 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B  72 
 HIS   0.013   0.001   HIS B 519 
 PHE   0.019   0.001   PHE B 517 
 TYR   0.011   0.001   TYR B 161 
 ARG   0.006   0.000   ARG A 530 

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

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

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 TYR cc_start: 0.8861 (t80) cc_final: 0.8640 (t80)
REVERT: A  339 LYS cc_start: 0.9420 (ptpp) cc_final: 0.9119 (ptpp)
REVERT: A  345 LEU cc_start: 0.9444 (mt) cc_final: 0.9095 (mt)
REVERT: A  362 LEU cc_start: 0.9147 (tp) cc_final: 0.8799 (tt)
REVERT: A  370 MET cc_start: 0.9283 (pmm) cc_final: 0.9062 (pmm)
REVERT: B  180 MET cc_start: 0.8068 (ptp) cc_final: 0.7525 (mpp)
REVERT: B  290 CYS cc_start: 0.9479 (m) cc_final: 0.9199 (m)
REVERT: B  489 LEU cc_start: 0.9544 (tt) cc_final: 0.9198 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2337
  time to fit residues: 19.2932
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 39 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3195 r_free = 0.3195 target = 0.058927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.037716 restraints weight = 104527.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.039486 restraints weight = 43609.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.040689 restraints weight = 26812.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2650 r_free = 0.2650    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8304  Z= 0.197
  Angle     :  0.630   8.849  11319  Z= 0.311
  Chirality :  0.040   0.156   1268
  Planarity :  0.005   0.044   1488
  Dihedral  :  6.598  87.140   1215
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -0.23 (0.25), residues: 1053
  helix:  0.63 (0.26), residues: 388
  sheet:  0.11 (0.37), residues: 185
  loop : -0.85 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  72 
 HIS   0.013   0.001   HIS B 519 
 PHE   0.018   0.001   PHE B 517 
 TYR   0.010   0.001   TYR B 161 
 ARG   0.007   0.000   ARG B 502 

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

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

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 TYR cc_start: 0.8922 (t80) cc_final: 0.8670 (t80)
REVERT: A  345 LEU cc_start: 0.9474 (mt) cc_final: 0.9186 (mt)
REVERT: A  362 LEU cc_start: 0.9144 (tp) cc_final: 0.8795 (tt)
REVERT: A  370 MET cc_start: 0.9313 (pmm) cc_final: 0.9092 (pmm)
REVERT: B  180 MET cc_start: 0.8074 (ptp) cc_final: 0.7533 (mpp)
REVERT: B  186 MET cc_start: 0.9077 (mmp) cc_final: 0.8825 (mmm)
REVERT: B  290 CYS cc_start: 0.9501 (m) cc_final: 0.9234 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2381
  time to fit residues: 18.3402
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0570
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.059602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.039249 restraints weight = 80840.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.040912 restraints weight = 37222.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.042012 restraints weight = 23793.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8304  Z= 0.158
  Angle     :  0.621   9.060  11319  Z= 0.306
  Chirality :  0.040   0.152   1268
  Planarity :  0.005   0.044   1488
  Dihedral  :  6.357  84.903   1215
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1053
  helix:  0.67 (0.26), residues: 385
  sheet:  0.04 (0.37), residues: 185
  loop : -0.82 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  72 
 HIS   0.012   0.001   HIS B 519 
 PHE   0.015   0.001   PHE B 517 
 TYR   0.011   0.001   TYR B 161 
 ARG   0.010   0.000   ARG A 207 

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

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

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 TYR cc_start: 0.8923 (t80) cc_final: 0.8672 (t80)
REVERT: A  345 LEU cc_start: 0.9465 (mt) cc_final: 0.9208 (mt)
REVERT: A  362 LEU cc_start: 0.9151 (tp) cc_final: 0.8803 (tt)
REVERT: A  370 MET cc_start: 0.9305 (pmm) cc_final: 0.9070 (pmm)
REVERT: B  180 MET cc_start: 0.8059 (ptp) cc_final: 0.7587 (mpp)
REVERT: B  290 CYS cc_start: 0.9469 (m) cc_final: 0.9196 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2778
  time to fit residues: 21.5785
Evaluate side-chains
  45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0980
   chunk 63 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3215 r_free = 0.3215 target = 0.059571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.038506 restraints weight = 106356.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.040226 restraints weight = 43714.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.041445 restraints weight = 26779.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8304  Z= 0.172
  Angle     :  0.628   8.718  11319  Z= 0.308
  Chirality :  0.040   0.150   1268
  Planarity :  0.005   0.051   1488
  Dihedral  :  6.285  89.326   1215
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -0.22 (0.25), residues: 1053
  helix:  0.65 (0.26), residues: 386
  sheet:  0.04 (0.37), residues: 185
  loop : -0.82 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B  72 
 HIS   0.011   0.001   HIS B 519 
 PHE   0.013   0.001   PHE B 517 
 TYR   0.012   0.001   TYR A 398 
 ARG   0.008   0.000   ARG B  39 

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

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

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2106 Ramachandran restraints generated.
    1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 TYR cc_start: 0.8977 (t80) cc_final: 0.8709 (t80)
REVERT: A  345 LEU cc_start: 0.9493 (mt) cc_final: 0.9225 (mt)
REVERT: A  362 LEU cc_start: 0.9127 (tp) cc_final: 0.8770 (tt)
REVERT: A  370 MET cc_start: 0.9333 (pmm) cc_final: 0.9103 (pmm)
REVERT: A  475 LYS cc_start: 0.9174 (ptmm) cc_final: 0.8974 (ptmm)
REVERT: B  180 MET cc_start: 0.8125 (ptp) cc_final: 0.7614 (mpp)
REVERT: B  186 MET cc_start: 0.9117 (mmp) cc_final: 0.8865 (mmm)
REVERT: B  290 CYS cc_start: 0.9490 (m) cc_final: 0.9203 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2453
  time to fit residues: 19.2241
Evaluate side-chains
  46 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 55.5665 > 50:
  distance: 23 - 190:  22.470
  distance: 32 - 168:  18.937
  distance: 73 - 201:   3.049
  distance: 82 - 179:  15.068
  distance: 85 - 176:   4.909
  distance: 94 - 166:  15.407
  distance: 97 - 163:  17.058
  distance: 120 - 121:   5.414
  distance: 122 - 123:   3.981
  distance: 122 - 127:  28.303
  distance: 124 - 125:   3.100
  distance: 127 - 128:  16.337
  distance: 128 - 131:  14.494
  distance: 129 - 130:   6.790
  distance: 129 - 132:  17.752
  distance: 132 - 133:   8.637
  distance: 133 - 134:  13.855
  distance: 133 - 136:   6.671
  distance: 134 - 135:  16.505
  distance: 134 - 138:  39.289
  distance: 136 - 137:   8.880
  distance: 138 - 139:  15.817
  distance: 139 - 140:  21.204
  distance: 139 - 142:  19.514
  distance: 140 - 141:   9.272
  distance: 140 - 144:  15.270
  distance: 142 - 143:  21.416
  distance: 144 - 145:  16.184
  distance: 145 - 146:  13.108
  distance: 145 - 148:   4.793
  distance: 146 - 147:   4.956
  distance: 146 - 155:  29.647
  distance: 148 - 149:  17.058
  distance: 155 - 156:  10.358
  distance: 156 - 157:   6.439
  distance: 156 - 159:   8.293
  distance: 157 - 158:   6.751
  distance: 157 - 163:  17.321
  distance: 159 - 160:   7.794
  distance: 163 - 164:  18.604
  distance: 164 - 165:   3.475
  distance: 164 - 167:  14.499
  distance: 165 - 166:   7.650
  distance: 165 - 168:  26.386
  distance: 168 - 169:  11.886
  distance: 169 - 170:   7.611
  distance: 169 - 172:   9.153
  distance: 170 - 171:   3.177
  distance: 170 - 176:   4.719
  distance: 172 - 173:   5.140
  distance: 176 - 177:   4.786
  distance: 177 - 178:   5.823
  distance: 177 - 180:   5.544
  distance: 178 - 179:  10.168
  distance: 178 - 190:  22.068
  distance: 180 - 181:   3.242
  distance: 190 - 191:  21.430
  distance: 191 - 192:  16.598
  distance: 191 - 194:   5.320
  distance: 192 - 193:  10.347
  distance: 192 - 201:   9.098
  distance: 194 - 195:   9.164
  distance: 195 - 196:   5.451
  distance: 195 - 197:   3.991