Starting phenix.real_space_refine
on Sun May 11 04:55:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kh4_37236/05_2025/8kh4_37236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kh4_37236/05_2025/8kh4_37236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kh4_37236/05_2025/8kh4_37236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kh4_37236/05_2025/8kh4_37236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kh4_37236/05_2025/8kh4_37236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kh4_37236/05_2025/8kh4_37236.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.118
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      51      5.16       5
     C    4814      2.51       5
     N    1286      2.21       5
     O    1370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7521
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2048
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2048
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 10, 'TRANS': 255}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 49
    Chain: "B"
      Number of atoms: 1809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1809
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 57
    Chain: "C"
      Number of atoms: 2435
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 336, 2425
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 113
      Conformer: "B"
        Number of residues, atoms: 336, 2425
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 113
          bond proxies already assigned to first conformer: 2458
    Chain: "E"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 936
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "D"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 265
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 1, 'TRANS': 42}
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 90
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.97, per 1000 atoms: 0.79
  Number of scatterers: 7521
  At special positions: 0
  Unit cell: (72.36, 95.04, 126.36, 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      51     16.00
     O    1370      8.00
     N    1286      7.00
     C    4814      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 178 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.03

  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: 2.17
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      43.4% alpha, 22.2% 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 27 through 55
      removed outlier: 3.838A  pdb=" N   ILE A  39 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ILE A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS A  55 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 59
    Processing helix  chain 'A' and resid 60 through 80
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 96 through 131
      removed outlier: 3.655A  pdb=" N   GLY A 119 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 139
    Processing helix  chain 'A' and resid 140 through 160
      removed outlier: 3.593A  pdb=" N   TRP A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 185 through 197
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.815A  pdb=" N   PHE A 201 " --> pdb=" O   ALA A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 297
      removed outlier: 3.683A  pdb=" N   PHE A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 302 through 327
      removed outlier: 4.122A  pdb=" N   ALA A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      Proline residue:  A 321  - end of helix
      removed outlier: 3.550A  pdb=" N   TRP A 327 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 338
    Processing helix  chain 'B' and resid 13 through 39
      removed outlier: 3.691A  pdb=" N   ALA B  39 " --> pdb=" O   GLN B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
      removed outlier: 3.658A  pdb=" N   MET B  60 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 279
    Processing helix  chain 'B' and resid 293 through 304
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 4.039A  pdb=" N   TYR B 311 " --> pdb=" O   LYS B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 318
    Processing helix  chain 'B' and resid 331 through 352
      removed outlier: 3.683A  pdb=" N   ILE B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   SER B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 391
    Processing helix  chain 'C' and resid 6 through 26
    Processing helix  chain 'C' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.739A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.563A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 24
    Processing helix  chain 'D' and resid 29 through 45
    Processing helix  chain 'D' and resid 46 through 48
      No H-bonds generated for 'chain 'D' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 172
      removed outlier: 3.657A  pdb=" N   VAL A 179 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASP A 172 " --> pdb=" O   MET A 177 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   MET A 177 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 214
      removed outlier: 9.660A  pdb=" N   ALA B 243 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ARG B  42 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   VAL B 247 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU B  46 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   ASP B 249 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE B 244 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   PHE B 290 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   PHE B 246 " --> pdb=" O   PHE B 290 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ASN B 292 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   VAL B 248 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52
      removed outlier: 3.625A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   PHE C 335 " --> pdb=" O   SER C 331 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL C 327 " --> pdb=" O   TRP C 339 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.692A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 4.555A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.579A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 7.112A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.737A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP C 254 " --> pdb=" O   GLN C 259 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.747A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.833A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 125 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   MET E  34 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ASP E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1212 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: 2.24

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1208
        1.29 -     1.42: 2106
        1.42 -     1.56: 4303
        1.56 -     1.69: 3
        1.69 -     1.83: 73
  Bond restraints: 7693
  Sorted by residual:
  bond pdb=" CA  PHE A 201 "
       pdb=" C   PHE A 201 "
    ideal  model  delta    sigma   weight residual
    1.524  1.415  0.109 1.29e-02 6.01e+03 7.08e+01
  bond pdb=" CA  SER A  62 "
       pdb=" C   SER A  62 "
    ideal  model  delta    sigma   weight residual
    1.524  1.426  0.098 1.26e-02 6.30e+03 6.04e+01
  bond pdb=" CA  VAL A 179 "
       pdb=" C   VAL A 179 "
    ideal  model  delta    sigma   weight residual
    1.523  1.427  0.096 1.27e-02 6.20e+03 5.74e+01
  bond pdb=" C   PHE A 201 "
       pdb=" O   PHE A 201 "
    ideal  model  delta    sigma   weight residual
    1.237  1.156  0.080 1.19e-02 7.06e+03 4.57e+01
  bond pdb=" N   VAL A 179 "
       pdb=" CA  VAL A 179 "
    ideal  model  delta    sigma   weight residual
    1.459  1.377  0.082 1.25e-02 6.40e+03 4.26e+01
  ... (remaining 7688 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 10227
        2.70 -     5.40: 217
        5.40 -     8.10: 39
        8.10 -    10.79: 14
       10.79 -    13.49: 6
  Bond angle restraints: 10503
  Sorted by residual:
  angle pdb=" N   ARG A 213 "
        pdb=" CA  ARG A 213 "
        pdb=" C   ARG A 213 "
      ideal   model   delta    sigma   weight residual
     111.07  100.56   10.51 1.07e+00 8.73e-01 9.65e+01
  angle pdb=" N   ILE A 211 "
        pdb=" CA  ILE A 211 "
        pdb=" C   ILE A 211 "
      ideal   model   delta    sigma   weight residual
     110.62  102.37    8.25 1.02e+00 9.61e-01 6.55e+01
  angle pdb=" N   ALA D  34 "
        pdb=" CA  ALA D  34 "
        pdb=" C   ALA D  34 "
      ideal   model   delta    sigma   weight residual
     111.28  102.51    8.77 1.09e+00 8.42e-01 6.47e+01
  angle pdb=" N   TYR D  40 "
        pdb=" CA  TYR D  40 "
        pdb=" C   TYR D  40 "
      ideal   model   delta    sigma   weight residual
     111.28  102.91    8.37 1.09e+00 8.42e-01 5.90e+01
  angle pdb=" C   PHE A 199 "
        pdb=" N   PRO A 200 "
        pdb=" CA  PRO A 200 "
      ideal   model   delta    sigma   weight residual
     119.05  110.58    8.47 1.11e+00 8.12e-01 5.82e+01
  ... (remaining 10498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.19: 4320
       24.19 -    48.38: 190
       48.38 -    72.57: 13
       72.57 -    96.76: 10
       96.76 -   120.95: 1
  Dihedral angle restraints: 4534
    sinusoidal: 1614
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" CB  CYS E  99 "
           pdb=" SG  CYS E  99 "
           pdb=" SG  CYS E 107 "
           pdb=" CB  CYS E 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -2.52  -83.48     1      1.00e+01 1.00e-02 8.51e+01
  dihedral pdb=" C   ASN A  63 "
           pdb=" N   ASN A  63 "
           pdb=" CA  ASN A  63 "
           pdb=" CB  ASN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.96   16.36     0      2.50e+00 1.60e-01 4.28e+01
  dihedral pdb=" N   ASN A  63 "
           pdb=" C   ASN A  63 "
           pdb=" CA  ASN A  63 "
           pdb=" CB  ASN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.06  -16.26     0      2.50e+00 1.60e-01 4.23e+01
  ... (remaining 4531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.163: 1181
       0.163 -    0.327: 29
       0.327 -    0.490: 7
       0.490 -    0.653: 4
       0.653 -    0.817: 2
  Chirality restraints: 1223
  Sorted by residual:
  chirality pdb=" CA  ASN A  63 "
            pdb=" N   ASN A  63 "
            pdb=" C   ASN A  63 "
            pdb=" CB  ASN A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.69    0.82 2.00e-01 2.50e+01 1.67e+01
  chirality pdb=" CA  ALA A 219 "
            pdb=" N   ALA A 219 "
            pdb=" C   ALA A 219 "
            pdb=" CB  ALA A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.77    0.72 2.00e-01 2.50e+01 1.28e+01
  chirality pdb=" CA  PHE A 174 "
            pdb=" N   PHE A 174 "
            pdb=" C   PHE A 174 "
            pdb=" CB  PHE A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.06e+01
  ... (remaining 1220 not shown)

  Planarity restraints: 1324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "    0.066 5.00e-02 4.00e+02   9.76e-02 1.53e+01
        pdb=" N   PRO C 236 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 213 "   -0.018 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   ARG A 213 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ARG A 213 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   VAL A 214 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  57 "    0.015 2.00e-02 2.50e+03   3.01e-02 9.07e+00
        pdb=" C   TYR A  57 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   TYR A  57 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A  58 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1321 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 128
        2.62 -     3.19: 6873
        3.19 -     3.76: 12272
        3.76 -     4.33: 16918
        4.33 -     4.90: 28357
  Nonbonded interactions: 64548
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A  61 "
            pdb=" CB  ALA A 144 "
     model   vdw
     2.049 3.880
  nonbonded pdb=" OG  SER C  74 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" N   VAL A 179 "
            pdb=" O   VAL A 179 "
     model   vdw
     2.218 2.496
  nonbonded pdb=" NH1 ARG B 228 "
            pdb=" OD1 ASP C 186 "
     model   vdw
     2.219 3.120
  ... (remaining 64543 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.770
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
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      :  0.009   0.109   7696  Z= 0.635
  Angle     :  1.017  13.493  10509  Z= 0.633
  Chirality :  0.081   0.817   1223
  Planarity :  0.007   0.098   1324
  Dihedral  : 14.018 120.945   2639
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.48 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.95 %
  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:  0.62 (0.27), residues: 988
  helix:  1.63 (0.26), residues: 402
  sheet:  0.16 (0.35), residues: 204
  loop : -0.73 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  99 
 HIS   0.007   0.002   HIS D  44 
 PHE   0.028   0.002   PHE A  65 
 TYR   0.025   0.002   TYR C  85 
 ARG   0.008   0.001   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12467 (  420)
  hydrogen bonds       : angle       6.80101 ( 1212)
  SS BOND              : bond        0.00782 (    3)
  SS BOND              : angle       3.09228 (    6)
  covalent geometry    : bond        0.00893 ( 7693)
  covalent geometry    : angle       1.01418 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 167
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.6682 (m-10)
REVERT: B   34 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7618 (tttt)
REVERT: B  280 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7821 (ttt90)
REVERT: B  317 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7476 (ptp90)
REVERT: C  101 MET cc_start: 0.8895 (mtp) cc_final: 0.8644 (mtp)
REVERT: C  290 ASP cc_start: 0.6802 (m-30) cc_final: 0.6572 (m-30)
REVERT: E   60 TYR cc_start: 0.7386 (m-80) cc_final: 0.7036 (m-80)
REVERT: E   80 TYR cc_start: 0.7486 (m-80) cc_final: 0.7066 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2147
  time to fit residues: 49.3000
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 49 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN
E  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.192886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.157791 restraints weight = 16004.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 3.53
r_work: 0.3704 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7696  Z= 0.183
  Angle     :  0.647  10.846  10509  Z= 0.340
  Chirality :  0.046   0.303   1223
  Planarity :  0.005   0.076   1324
  Dihedral  :  5.920  56.992   1149
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.36 %
    Favored  : 88.56 %
  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:  0.76 (0.27), residues: 988
  helix:  1.93 (0.27), residues: 384
  sheet:  0.05 (0.33), residues: 222
  loop : -0.65 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  99 
 HIS   0.005   0.001   HIS C 225 
 PHE   0.018   0.002   PHE B 212 
 TYR   0.032   0.002   TYR C  85 
 ARG   0.005   0.001   ARG C 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  420)
  hydrogen bonds       : angle       5.38077 ( 1212)
  SS BOND              : bond        0.00193 (    3)
  SS BOND              : angle       1.90972 (    6)
  covalent geometry    : bond        0.00417 ( 7693)
  covalent geometry    : angle       0.64587 (10503)

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

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

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1976 Ramachandran restraints generated.
    988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.6246 (ppp)
REVERT: A  327 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.6973 (m-10)
REVERT: B  266 LEU cc_start: 0.8546 (tp) cc_final: 0.8201 (tp)
REVERT: B  274 LYS cc_start: 0.7903 (tttp) cc_final: 0.7625 (ttmt)
REVERT: B  280 ARG cc_start: 0.8277 (tpt90) cc_final: 0.7978 (ttt90)
REVERT: E   80 TYR cc_start: 0.7761 (m-80) cc_final: 0.7192 (m-80)
REVERT: E   93 VAL cc_start: 0.7450 (t) cc_final: 0.7178 (t)
REVERT: E  115 TYR cc_start: 0.8110 (t80) cc_final: 0.7889 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 160
  average time/residue: 0.2220
  time to fit residues: 47.8321
Evaluate side-chains
  150 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  327 TRP
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain B residue  284 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 69.9422 > 50:
  distance: 144 - 150:  34.754
  distance: 150 - 151:  39.374
  distance: 151 - 152:  42.529
  distance: 151 - 154:  39.051
  distance: 152 - 153:  49.628
  distance: 152 - 161:  22.027
  distance: 154 - 155:  56.552
  distance: 155 - 156:  42.201
  distance: 156 - 157:  47.569
  distance: 157 - 158:  50.079
  distance: 158 - 159:  28.360
  distance: 158 - 160:  15.113
  distance: 161 - 162:  24.530
  distance: 162 - 163:   6.770
  distance: 162 - 165:  29.393
  distance: 163 - 164:  45.855
  distance: 163 - 168:  52.429
  distance: 165 - 166:  46.269
  distance: 165 - 167:  44.074
  distance: 168 - 169:  44.099
  distance: 169 - 170:  18.275
  distance: 169 - 172:  22.200
  distance: 170 - 171:  24.735
  distance: 170 - 174:  36.381
  distance: 172 - 173:  32.169
  distance: 174 - 175:  11.630
  distance: 174 - 259:  31.505
  distance: 175 - 176:  38.195
  distance: 175 - 178:  47.936
  distance: 176 - 177:  34.806
  distance: 176 - 180:  18.501
  distance: 177 - 256:  32.472
  distance: 178 - 179:  55.358
  distance: 180 - 181:  25.995
  distance: 181 - 182:  20.988
  distance: 181 - 184:  48.115
  distance: 182 - 183:  48.735
  distance: 182 - 188:   9.092
  distance: 184 - 185:  16.224
  distance: 185 - 186:  31.991
  distance: 185 - 187:  33.274
  distance: 188 - 189:  23.222
  distance: 188 - 248:  19.467
  distance: 189 - 190:  56.973
  distance: 190 - 191:  49.291
  distance: 190 - 192:  32.592
  distance: 191 - 245:  28.593
  distance: 192 - 193:  40.106
  distance: 193 - 194:  48.438
  distance: 193 - 196:  41.720
  distance: 194 - 195:  56.574
  distance: 194 - 199:  46.984
  distance: 196 - 197:  50.588
  distance: 196 - 198:   8.831
  distance: 199 - 200:  49.324
  distance: 200 - 201:  39.283
  distance: 200 - 203:  14.443
  distance: 201 - 206:   7.686
  distance: 203 - 204:  43.229
  distance: 203 - 205:  35.464
  distance: 206 - 207:  27.965
  distance: 207 - 208:  44.428
  distance: 207 - 210:  47.809
  distance: 208 - 209:  43.964
  distance: 208 - 214:  38.957
  distance: 210 - 211:  49.829
  distance: 211 - 212:  12.243
  distance: 211 - 213:  41.395
  distance: 214 - 215:   7.172
  distance: 215 - 216:  48.036
  distance: 215 - 218:  42.107
  distance: 216 - 217:  47.269
  distance: 216 - 222:  34.680
  distance: 218 - 219:  57.299
  distance: 219 - 220:  50.101
  distance: 219 - 221:  41.929