Starting phenix.real_space_refine
on Sat Aug 23 03:32:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9luc_63394/08_2025/9luc_63394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9luc_63394/08_2025/9luc_63394.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9luc_63394/08_2025/9luc_63394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9luc_63394/08_2025/9luc_63394.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9luc_63394/08_2025/9luc_63394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9luc_63394/08_2025/9luc_63394.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
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      50      5.16       5
     C    6168      2.51       5
     N    1588      2.21       5
     O    1778      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9584
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1685
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
    Chain: "B"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1685
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
    Chain: "E"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1866
          Classifications: {'peptide': 246}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "A"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1694
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 211}
    Chain: "D"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1866
          Classifications: {'peptide': 246}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "F"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 389
          Classifications: {'peptide': 47}
          Link IDs: {'TRANS': 46}
    Chain: "G"
      Number of atoms: 399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 399
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
  Time building chain proxies: 2.42, per 1000 atoms: 0.25
  Number of scatterers: 9584
  At special positions: 0
  Unit cell: (89.76, 88.88, 110.88, 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      50     16.00
     O    1778      8.00
     N    1588      7.00
     C    6168      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 372.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2302

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 0 sheets defined
      91.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'C' and resid 33 through 51
    Processing helix  chain 'C' and resid 52 through 57
    Processing helix  chain 'C' and resid 58 through 67
    Processing helix  chain 'C' and resid 73 through 92
      removed outlier: 4.090A  pdb=" N   GLU C  79 " --> pdb=" O   ASN C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 101
      removed outlier: 4.227A  pdb=" N   LYS C  99 " --> pdb=" O   ALA C  95 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU C 101 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 117
    Processing helix  chain 'C' and resid 120 through 169
      removed outlier: 3.900A  pdb=" N   ASP C 131 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU C 145 " --> pdb=" O   ASN C 141 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE C 146 " --> pdb=" O   TYR C 142 " (cutoff:3.500A)
      Proline residue:  C 154  - end of helix
    Processing helix  chain 'C' and resid 170 through 172
      No H-bonds generated for 'chain 'C' and resid 170 through 172'
    Processing helix  chain 'C' and resid 174 through 186
      removed outlier: 3.577A  pdb=" N   LEU C 178 " --> pdb=" O   ASP C 174 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY C 179 " --> pdb=" O   PRO C 175 " (cutoff:3.500A)
      Proline residue:  C 180  - end of helix
    Processing helix  chain 'C' and resid 186 through 199
      removed outlier: 3.640A  pdb=" N   ALA C 196 " --> pdb=" O   GLY C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 231
      removed outlier: 3.594A  pdb=" N   GLU C 213 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU C 214 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   VAL C 217 " --> pdb=" O   GLU C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 242
      removed outlier: 3.505A  pdb=" N   ASN C 242 " --> pdb=" O   ARG C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 245
      No H-bonds generated for 'chain 'C' and resid 243 through 245'
    Processing helix  chain 'B' and resid 27 through 31
      removed outlier: 3.996A  pdb=" N   PHE B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 51
    Processing helix  chain 'B' and resid 52 through 57
      removed outlier: 3.632A  pdb=" N   ILE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 67
      removed outlier: 3.707A  pdb=" N   GLY B  62 " --> pdb=" O   THR B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 89
      removed outlier: 3.595A  pdb=" N   ASP B  80 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 95
    Processing helix  chain 'B' and resid 96 through 101
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 3.544A  pdb=" N   VAL B 115 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 169
      removed outlier: 3.770A  pdb=" N   LEU B 130 " --> pdb=" O   GLN B 126 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASP B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR B 142 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 146 " --> pdb=" O   TYR B 142 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
    Processing helix  chain 'B' and resid 170 through 172
      No H-bonds generated for 'chain 'B' and resid 170 through 172'
    Processing helix  chain 'B' and resid 177 through 199
      removed outlier: 3.526A  pdb=" N   VAL B 184 " --> pdb=" O   PRO B 180 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   THR B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA B 196 " --> pdb=" O   GLY B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 231
      removed outlier: 3.748A  pdb=" N   GLU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU B 214 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 242
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'E' and resid 2 through 23
      removed outlier: 3.534A  pdb=" N   PHE E  20 " --> pdb=" O   ILE E  16 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 31
      removed outlier: 3.516A  pdb=" N   PHE E  31 " --> pdb=" O   THR E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 51
    Processing helix  chain 'E' and resid 52 through 57
    Processing helix  chain 'E' and resid 58 through 67
    Processing helix  chain 'E' and resid 73 through 89
      removed outlier: 4.320A  pdb=" N   GLU E  79 " --> pdb=" O   ASN E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 99
      removed outlier: 4.239A  pdb=" N   LEU E  96 " --> pdb=" O   GLY E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 105 through 117
    Processing helix  chain 'E' and resid 120 through 169
      removed outlier: 3.992A  pdb=" N   GLN E 126 " --> pdb=" O   PRO E 122 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS E 135 " --> pdb=" O   ASP E 131 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   LEU E 145 " --> pdb=" O   ASN E 141 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   PHE E 146 " --> pdb=" O   TYR E 142 " (cutoff:3.500A)
      Proline residue:  E 154  - end of helix
      removed outlier: 4.056A  pdb=" N   MET E 163 " --> pdb=" O   ILE E 159 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLN E 167 " --> pdb=" O   MET E 163 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 172
      No H-bonds generated for 'chain 'E' and resid 170 through 172'
    Processing helix  chain 'E' and resid 174 through 199
      removed outlier: 4.436A  pdb=" N   GLY E 179 " --> pdb=" O   PRO E 175 " (cutoff:3.500A)
      Proline residue:  E 180  - end of helix
      removed outlier: 3.661A  pdb=" N   ALA E 183 " --> pdb=" O   GLY E 179 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL E 184 " --> pdb=" O   PRO E 180 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ALA E 185 " --> pdb=" O   SER E 181 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   PHE E 186 " --> pdb=" O   ILE E 182 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR E 189 " --> pdb=" O   ALA E 185 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA E 196 " --> pdb=" O   GLY E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 231
      removed outlier: 3.682A  pdb=" N   GLU E 213 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 242
    Processing helix  chain 'E' and resid 243 through 245
      No H-bonds generated for 'chain 'E' and resid 243 through 245'
    Processing helix  chain 'A' and resid 32 through 51
      removed outlier: 3.668A  pdb=" N   ILE A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 3.814A  pdb=" N   ILE A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'A' and resid 73 through 91
      removed outlier: 4.180A  pdb=" N   GLU A  79 " --> pdb=" O   ASN A  75 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 102
      removed outlier: 3.861A  pdb=" N   GLU A  97 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLN A  98 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A  99 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 120 through 171
      removed outlier: 3.792A  pdb=" N   ASP A 131 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   PHE A 146 " --> pdb=" O   TYR A 142 " (cutoff:3.500A)
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 177 through 199
      removed outlier: 3.763A  pdb=" N   ILE A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ALA A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   THR A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 231
      removed outlier: 3.928A  pdb=" N   GLU A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 243
      removed outlier: 3.650A  pdb=" N   THR A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 23
    Processing helix  chain 'D' and resid 26 through 30
    Processing helix  chain 'D' and resid 32 through 51
    Processing helix  chain 'D' and resid 52 through 57
      removed outlier: 3.582A  pdb=" N   ILE D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 67
      removed outlier: 3.505A  pdb=" N   GLY D  62 " --> pdb=" O   THR D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 92
      removed outlier: 4.101A  pdb=" N   GLU D  79 " --> pdb=" O   ASN D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 100
      removed outlier: 4.064A  pdb=" N   LYS D  99 " --> pdb=" O   ALA D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 117
    Processing helix  chain 'D' and resid 120 through 171
      removed outlier: 4.084A  pdb=" N   ASP D 131 " --> pdb=" O   ILE D 127 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LEU D 145 " --> pdb=" O   ASN D 141 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   PHE D 146 " --> pdb=" O   TYR D 142 " (cutoff:3.500A)
      Proline residue:  D 154  - end of helix
    Processing helix  chain 'D' and resid 177 through 186
      removed outlier: 4.620A  pdb=" N   SER D 181 " --> pdb=" O   GLN D 177 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA D 185 " --> pdb=" O   SER D 181 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   PHE D 186 " --> pdb=" O   ILE D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 199
      removed outlier: 3.663A  pdb=" N   ALA D 196 " --> pdb=" O   GLY D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 231
      removed outlier: 4.092A  pdb=" N   VAL D 217 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN D 229 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 242
      removed outlier: 3.620A  pdb=" N   ASN D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 245
      No H-bonds generated for 'chain 'D' and resid 243 through 245'
    Processing helix  chain 'F' and resid 16 through 39
      removed outlier: 3.971A  pdb=" N   ILE F  20 " --> pdb=" O   ASP F  16 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR F  21 " --> pdb=" O   ARG F  17 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ASP F  24 " --> pdb=" O   ILE F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 43 through 58
      removed outlier: 3.573A  pdb=" N   THR F  56 " --> pdb=" O   SER F  52 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 13 through 17
    Processing helix  chain 'G' and resid 18 through 40
      removed outlier: 3.849A  pdb=" N   MET G  39 " --> pdb=" O   MET G  35 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER G  40 " --> pdb=" O   MET G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 43 through 59
      removed outlier: 3.647A  pdb=" N   THR G  56 " --> pdb=" O   SER G  52 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   THR G  57 " --> pdb=" O   SER G  53 " (cutoff:3.500A)

    763 hydrogen bonds defined for protein.
    2250 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1996
        1.33 -     1.46: 2953
        1.46 -     1.59: 4689
        1.59 -     1.72: 0
        1.72 -     1.85: 100
  Bond restraints: 9738
  Sorted by residual:
  bond pdb=" C   PHE F  58 "
       pdb=" O   PHE F  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.470 -0.234 1.29e-02 6.01e+03 3.29e+02
  bond pdb=" C   ALA C  46 "
       pdb=" N   VAL C  47 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.063 1.26e-02 6.30e+03 2.47e+01
  bond pdb=" CA  ALA C  46 "
       pdb=" C   ALA C  46 "
    ideal  model  delta    sigma   weight residual
    1.523  1.580 -0.057 1.30e-02 5.92e+03 1.91e+01
  bond pdb=" C   PHE G  58 "
       pdb=" O   PHE G  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.284 -0.048 1.32e-02 5.74e+03 1.32e+01
  bond pdb=" CA  ALA A 143 "
       pdb=" CB  ALA A 143 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.053 1.66e-02 3.63e+03 1.02e+01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.17: 13144
        5.17 -    10.34: 59
       10.34 -    15.52: 1
       15.52 -    20.69: 1
       20.69 -    25.86: 2
  Bond angle restraints: 13207
  Sorted by residual:
  angle pdb=" CA  PHE G  58 "
        pdb=" C   PHE G  58 "
        pdb=" O   PHE G  58 "
      ideal   model   delta    sigma   weight residual
     119.18   93.79   25.39 1.19e+00 7.06e-01 4.55e+02
  angle pdb=" O   PHE G  58 "
        pdb=" C   PHE G  58 "
        pdb=" N   GLN G  59 "
      ideal   model   delta    sigma   weight residual
     122.41  148.27  -25.86 1.42e+00 4.96e-01 3.32e+02
  angle pdb=" CA  ALA C  46 "
        pdb=" C   ALA C  46 "
        pdb=" N   VAL C  47 "
      ideal   model   delta    sigma   weight residual
     117.30  132.97  -15.67 1.16e+00 7.43e-01 1.83e+02
  angle pdb=" CA  ALA C  46 "
        pdb=" C   ALA C  46 "
        pdb=" O   ALA C  46 "
      ideal   model   delta    sigma   weight residual
     120.55  111.40    9.15 1.06e+00 8.90e-01 7.45e+01
  angle pdb=" O   ALA C  46 "
        pdb=" C   ALA C  46 "
        pdb=" N   VAL C  47 "
      ideal   model   delta    sigma   weight residual
     122.12  114.96    7.16 1.06e+00 8.90e-01 4.56e+01
  ... (remaining 13202 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 5142
       17.57 -    35.15: 466
       35.15 -    52.72: 203
       52.72 -    70.30: 54
       70.30 -    87.87: 21
  Dihedral angle restraints: 5886
    sinusoidal: 2311
      harmonic: 3575
  Sorted by residual:
  dihedral pdb=" CD  ARG A  89 "
           pdb=" NE  ARG A  89 "
           pdb=" CZ  ARG A  89 "
           pdb=" NH1 ARG A  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.26  -80.26     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CD  ARG G  41 "
           pdb=" NE  ARG G  41 "
           pdb=" CZ  ARG G  41 "
           pdb=" NH1 ARG G  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   72.87  -72.87     1      1.00e+01 1.00e-02 6.77e+01
  dihedral pdb=" CD  ARG G  17 "
           pdb=" NE  ARG G  17 "
           pdb=" CZ  ARG G  17 "
           pdb=" NH1 ARG G  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.44  -70.44     1      1.00e+01 1.00e-02 6.39e+01
  ... (remaining 5883 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1106
       0.086 -    0.171: 414
       0.171 -    0.257: 64
       0.257 -    0.343: 7
       0.343 -    0.428: 2
  Chirality restraints: 1593
  Sorted by residual:
  chirality pdb=" CA  ASP E 133 "
            pdb=" N   ASP E 133 "
            pdb=" C   ASP E 133 "
            pdb=" CB  ASP E 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.59e+00
  chirality pdb=" CA  ALA C  46 "
            pdb=" N   ALA C  46 "
            pdb=" C   ALA C  46 "
            pdb=" CB  ALA C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.06    0.43 2.00e-01 2.50e+01 4.54e+00
  chirality pdb=" CA  ASN C 197 "
            pdb=" N   ASN C 197 "
            pdb=" C   ASN C 197 "
            pdb=" CB  ASN C 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 1590 not shown)

  Planarity restraints: 1673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  41 "    1.138 9.50e-02 1.11e+02   5.11e-01 1.68e+02
        pdb=" NE  ARG G  41 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  41 "   -0.071 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  41 "    0.029 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  41 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  89 "   -1.038 9.50e-02 1.11e+02   4.65e-01 1.35e+02
        pdb=" NE  ARG A  89 "    0.075 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  89 "   -0.026 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  89 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  89 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  17 "   -0.960 9.50e-02 1.11e+02   4.31e-01 1.18e+02
        pdb=" NE  ARG G  17 "    0.073 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  17 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  17 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  17 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1670 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1402
        2.77 -     3.30: 10488
        3.30 -     3.84: 15450
        3.84 -     4.37: 18281
        4.37 -     4.90: 30050
  Nonbonded interactions: 75671
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 197 "
            pdb=" NH2 ARG F  17 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASP A 174 "
            pdb=" N   SER A 176 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" NZ  LYS B 206 "
            pdb=" O   ILE A  49 "
     model   vdw
     2.430 3.120
  nonbonded pdb=" O   SER B 176 "
            pdb=" OG  SER F  53 "
     model   vdw
     2.431 3.040
  nonbonded pdb=" O   LEU D 172 "
            pdb=" C   THR D 173 "
     model   vdw
     2.439 3.270
  ... (remaining 75666 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 27 through 246)
  selection = chain 'B'
  selection = chain 'C'
  selection = (chain 'D' and resid 27 through 246)
  selection = (chain 'E' and resid 27 through 246)
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and resid 14 through 60)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.740
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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      :  0.010   0.234   9738  Z= 0.634
  Angle     :  1.490  25.860  13207  Z= 0.988
  Chirality :  0.086   0.428   1593
  Planarity :  0.032   0.511   1673
  Dihedral  : 17.826  87.872   3584
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.59 %
    Favored  : 97.33 %
  Rotamer:
    Outliers : 11.92 %
    Allowed  :  6.78 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.22), residues: 1235
  helix: -0.89 (0.14), residues: 1026
  sheet:  None (None), residues: 0
  loop :  0.17 (0.50), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.063   0.008   ARG A 238 
 TYR   0.068   0.012   TYR B  51 
 PHE   0.045   0.009   PHE A 146 
 TRP   0.034   0.009   TRP C  77 
 HIS   0.020   0.005   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00972 ( 9738)
  covalent geometry    : angle       1.48964 (13207)
  hydrogen bonds       : bond        0.22476 (  763)
  hydrogen bonds       : angle       8.42119 ( 2250)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  439 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 123
    poor density    : 316
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   79 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8736 (mm-30)
REVERT: C  156 MET cc_start: 0.9027 (mmt) cc_final: 0.8783 (mmt)
REVERT: C  177 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7266 (tp40)
REVERT: C  213 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8394 (tm-30)
REVERT: B   89 ARG cc_start: 0.8405 (mmm160) cc_final: 0.7714 (mtm-85)
REVERT: B  117 ASP cc_start: 0.8540 (m-30) cc_final: 0.8264 (m-30)
REVERT: B  156 MET cc_start: 0.9049 (mmp) cc_final: 0.8745 (mmp)
REVERT: B  239 LYS cc_start: 0.9341 (tppt) cc_final: 0.8966 (ttpt)
REVERT: E   32 GLN cc_start: 0.8543 (tt0) cc_final: 0.8212 (tp40)
REVERT: E   64 LYS cc_start: 0.8181 (tptt) cc_final: 0.7841 (mttm)
REVERT: E  110 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8502 (tt0)
REVERT: E  156 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8591 (mmm)
REVERT: A   68 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8254 (pttp)
REVERT: A   83 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8629 (tm-30)
REVERT: A   97 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8602 (pp20)
REVERT: A  110 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8695 (mp0)
REVERT: A  119 THR cc_start: 0.8523 (p) cc_final: 0.8222 (p)
REVERT: A  233 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6865 (p0)
REVERT: D   27 ILE cc_start: 0.8378 (mp) cc_final: 0.7987 (mt)
REVERT: D   89 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7201 (ttm-80)
REVERT: D  177 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6918 (tm-30)
REVERT: D  205 SER cc_start: 0.9140 (t) cc_final: 0.8746 (p)
REVERT: D  213 GLU cc_start: 0.9507 (OUTLIER) cc_final: 0.9050 (mt-10)
REVERT: F   49 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8133 (tp30)
REVERT: G   17 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8467 (ptp-170)
REVERT: G   49 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6587 (mt-10)
  outliers start: 123
  outliers final: 48
  residues processed: 397
  average time/residue: 0.1202
  time to fit residues: 63.3348
Evaluate side-chains
  273 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 212
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain E residue  110 GLU
Chi-restraints excluded: chain E residue  156 MET
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   32 GLN
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  177 GLN
Chi-restraints excluded: chain D residue  182 ILE
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain F residue   19 MET
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   39 MET
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   43 ASP
Chi-restraints excluded: chain F residue   45 SER
Chi-restraints excluded: chain F residue   49 GLU
Chi-restraints excluded: chain F residue   58 PHE
Chi-restraints excluded: chain G residue   13 SER
Chi-restraints excluded: chain G residue   17 ARG
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   39 MET
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   43 ASP
Chi-restraints excluded: chain G residue   49 GLU
Chi-restraints excluded: chain G residue   50 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C  98 GLN
B 113 GLN
B 167 GLN
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
E 197 ASN
A  75 ASN
A 177 GLN
A 197 ASN
D  32 GLN
D  54 HIS
D  70 ASN
** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 177 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.120571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.093393 restraints weight = 14092.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.097331 restraints weight = 6559.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.099910 restraints weight = 4173.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.101425 restraints weight = 3194.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.102356 restraints weight = 2736.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9738  Z= 0.152
  Angle     :  0.616   7.618  13207  Z= 0.323
  Chirality :  0.041   0.133   1593
  Planarity :  0.005   0.052   1673
  Dihedral  : 11.259  75.834   1453
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 14.34 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.24), residues: 1235
  helix:  1.36 (0.16), residues: 1061
  sheet:  None (None), residues: 0
  loop : -0.48 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 109 
 TYR   0.014   0.002   TYR C 191 
 PHE   0.014   0.001   PHE D  31 
 TRP   0.015   0.001   TRP G  18 
 HIS   0.026   0.001   HIS D 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9738)
  covalent geometry    : angle       0.61565 (13207)
  hydrogen bonds       : bond        0.05715 (  763)
  hydrogen bonds       : angle       4.56449 ( 2250)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 231
  time to evaluate  : 0.379 
Fit side-chains
REVERT: C   50 SER cc_start: 0.9425 (t) cc_final: 0.8681 (p)
REVERT: C   98 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8522 (mm-40)
REVERT: C  124 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7590 (p)
REVERT: C  177 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7452 (mm-40)
REVERT: B   76 GLU cc_start: 0.7443 (mp0) cc_final: 0.7031 (mp0)
REVERT: B   89 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7381 (ttp80)
REVERT: B  140 ASP cc_start: 0.8347 (t70) cc_final: 0.7818 (t0)
REVERT: B  156 MET cc_start: 0.8959 (mmp) cc_final: 0.8665 (mmp)
REVERT: B  239 LYS cc_start: 0.9109 (tppt) cc_final: 0.8327 (ttpt)
REVERT: E   64 LYS cc_start: 0.7830 (tptt) cc_final: 0.7489 (mttm)
REVERT: E   71 ARG cc_start: 0.6851 (mmm160) cc_final: 0.6539 (mtt180)
REVERT: E  126 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8219 (tm-30)
REVERT: E  167 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8035 (tp-100)
REVERT: A   57 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8214 (mtt90)
REVERT: A   70 ASN cc_start: 0.8131 (p0) cc_final: 0.7289 (t0)
REVERT: A   83 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8113 (tm-30)
REVERT: A  205 SER cc_start: 0.8370 (t) cc_final: 0.8003 (p)
REVERT: A  206 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8153 (tttt)
REVERT: A  218 MET cc_start: 0.8634 (mtt) cc_final: 0.8401 (mtp)
REVERT: A  233 ASN cc_start: 0.5791 (OUTLIER) cc_final: 0.5159 (p0)
REVERT: D   10 ILE cc_start: 0.8026 (mm) cc_final: 0.7803 (mt)
REVERT: D  174 ASP cc_start: 0.7463 (m-30) cc_final: 0.7164 (m-30)
REVERT: D  213 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7959 (mt-10)
REVERT: F   19 MET cc_start: 0.7895 (ptp) cc_final: 0.7680 (ptt)
REVERT: G   49 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6415 (mt-10)
  outliers start: 67
  outliers final: 24
  residues processed: 274
  average time/residue: 0.1110
  time to fit residues: 41.4205
Evaluate side-chains
  229 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  233 ASN
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain D residue  147 GLU
Chi-restraints excluded: chain D residue  181 SER
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   49 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 116 optimal weight:    0.5980
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 108 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 121 GLN
B 229 GLN
E 171 HIS
A  75 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.094860 restraints weight = 13927.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098709 restraints weight = 6449.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.101247 restraints weight = 4071.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.102703 restraints weight = 3114.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.103660 restraints weight = 2674.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9738  Z= 0.130
  Angle     :  0.546   8.712  13207  Z= 0.280
  Chirality :  0.038   0.148   1593
  Planarity :  0.004   0.045   1673
  Dihedral  :  7.346  64.316   1362
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.54 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.57 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.25), residues: 1235
  helix:  2.00 (0.16), residues: 1052
  sheet:  None (None), residues: 0
  loop : -0.28 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  41 
 TYR   0.013   0.001   TYR F  47 
 PHE   0.013   0.001   PHE G  33 
 TRP   0.007   0.001   TRP E  77 
 HIS   0.004   0.001   HIS D  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9738)
  covalent geometry    : angle       0.54609 (13207)
  hydrogen bonds       : bond        0.04733 (  763)
  hydrogen bonds       : angle       4.06497 ( 2250)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 214
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: C  117 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7267 (m-30)
REVERT: C  177 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7407 (mm-40)
REVERT: B   73 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6660 (pm20)
REVERT: B   77 TRP cc_start: 0.8812 (m-10) cc_final: 0.8186 (m-90)
REVERT: B   86 MET cc_start: 0.8307 (mmm) cc_final: 0.7459 (mtm)
REVERT: B  239 LYS cc_start: 0.9063 (tppt) cc_final: 0.8342 (ttpt)
REVERT: E   64 LYS cc_start: 0.7787 (tptt) cc_final: 0.7422 (mttm)
REVERT: E  113 GLN cc_start: 0.8236 (mt0) cc_final: 0.7999 (mt0)
REVERT: E  156 MET cc_start: 0.9115 (mpp) cc_final: 0.8697 (mmm)
REVERT: E  219 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8099 (mt-10)
REVERT: A  163 MET cc_start: 0.8231 (mmm) cc_final: 0.7904 (mmm)
REVERT: A  205 SER cc_start: 0.8339 (t) cc_final: 0.8090 (p)
REVERT: A  206 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8243 (tttt)
REVERT: A  218 MET cc_start: 0.8664 (mtt) cc_final: 0.8451 (mtm)
REVERT: A  220 MET cc_start: 0.8668 (ttp) cc_final: 0.8351 (tmm)
REVERT: A  233 ASN cc_start: 0.5748 (OUTLIER) cc_final: 0.5208 (p0)
REVERT: D   10 ILE cc_start: 0.8041 (mm) cc_final: 0.7807 (mt)
REVERT: D  174 ASP cc_start: 0.7502 (m-30) cc_final: 0.7189 (m-30)
REVERT: D  213 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7838 (mt-10)
REVERT: F   19 MET cc_start: 0.7865 (ptp) cc_final: 0.7569 (ptt)
REVERT: F   41 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7518 (mtm-85)
  outliers start: 37
  outliers final: 22
  residues processed: 241
  average time/residue: 0.1022
  time to fit residues: 33.6222
Evaluate side-chains
  225 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  147 GLU
Chi-restraints excluded: chain D residue  181 SER
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 121 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094363 restraints weight = 14482.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098126 restraints weight = 6910.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.100555 restraints weight = 4460.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.101937 restraints weight = 3461.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102608 restraints weight = 3009.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9738  Z= 0.124
  Angle     :  0.540   8.215  13207  Z= 0.273
  Chirality :  0.038   0.134   1593
  Planarity :  0.004   0.046   1673
  Dihedral  :  6.025  64.162   1348
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.78 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.22 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.25), residues: 1235
  helix:  2.21 (0.16), residues: 1050
  sheet:  None (None), residues: 0
  loop : -0.36 (0.47), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  90 
 TYR   0.013   0.001   TYR G  47 
 PHE   0.015   0.001   PHE D  31 
 TRP   0.009   0.001   TRP E  77 
 HIS   0.007   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9738)
  covalent geometry    : angle       0.54025 (13207)
  hydrogen bonds       : bond        0.04389 (  763)
  hydrogen bonds       : angle       3.88250 ( 2250)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 207
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7791 (ttmt)
REVERT: C  117 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7197 (m-30)
REVERT: B   68 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8575 (ttmm)
REVERT: B   73 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6595 (pm20)
REVERT: B   77 TRP cc_start: 0.8780 (m-10) cc_final: 0.8269 (m-90)
REVERT: B  191 TYR cc_start: 0.8753 (m-10) cc_final: 0.8448 (m-10)
REVERT: E   64 LYS cc_start: 0.7823 (tptt) cc_final: 0.7496 (mttm)
REVERT: E  113 GLN cc_start: 0.8134 (mt0) cc_final: 0.7875 (mt0)
REVERT: E  128 MET cc_start: 0.8837 (mmm) cc_final: 0.8549 (mtp)
REVERT: E  156 MET cc_start: 0.9129 (mpp) cc_final: 0.8683 (mmm)
REVERT: E  219 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8008 (mt-10)
REVERT: A   70 ASN cc_start: 0.7983 (p0) cc_final: 0.7189 (t0)
REVERT: A  205 SER cc_start: 0.8448 (t) cc_final: 0.8173 (p)
REVERT: A  206 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8342 (tttt)
REVERT: A  218 MET cc_start: 0.8689 (mtt) cc_final: 0.8440 (mtm)
REVERT: A  220 MET cc_start: 0.8751 (ttp) cc_final: 0.8523 (tmm)
REVERT: A  233 ASN cc_start: 0.5798 (OUTLIER) cc_final: 0.5250 (p0)
REVERT: D   10 ILE cc_start: 0.8132 (mm) cc_final: 0.7920 (mt)
REVERT: D  117 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7863 (t0)
REVERT: D  174 ASP cc_start: 0.7474 (m-30) cc_final: 0.7207 (m-30)
REVERT: D  213 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7798 (mt-10)
REVERT: F   19 MET cc_start: 0.7800 (ptp) cc_final: 0.7472 (ptt)
  outliers start: 32
  outliers final: 20
  residues processed: 227
  average time/residue: 0.0933
  time to fit residues: 29.1199
Evaluate side-chains
  223 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  117 ASP
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.092532 restraints weight = 14486.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.096161 restraints weight = 6996.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.098527 restraints weight = 4565.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.099930 restraints weight = 3564.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.100587 restraints weight = 3095.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9738  Z= 0.135
  Angle     :  0.550   7.459  13207  Z= 0.277
  Chirality :  0.038   0.140   1593
  Planarity :  0.004   0.046   1673
  Dihedral  :  5.766  64.926   1344
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.70 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.61 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.87 (0.25), residues: 1235
  helix:  2.29 (0.16), residues: 1049
  sheet:  None (None), residues: 0
  loop : -0.38 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  71 
 TYR   0.010   0.001   TYR A  51 
 PHE   0.011   0.001   PHE D  31 
 TRP   0.005   0.001   TRP E  77 
 HIS   0.009   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9738)
  covalent geometry    : angle       0.55022 (13207)
  hydrogen bonds       : bond        0.04463 (  763)
  hydrogen bonds       : angle       3.86609 ( 2250)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7742 (ttmt)
REVERT: C  117 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7229 (m-30)
REVERT: B   68 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8581 (ttmm)
REVERT: B   73 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6574 (pm20)
REVERT: B   77 TRP cc_start: 0.8766 (m-10) cc_final: 0.8198 (m-90)
REVERT: B   86 MET cc_start: 0.8352 (mmm) cc_final: 0.7378 (mtm)
REVERT: B  191 TYR cc_start: 0.8726 (m-10) cc_final: 0.8457 (m-10)
REVERT: B  239 LYS cc_start: 0.9292 (tppt) cc_final: 0.8223 (ttpt)
REVERT: E   64 LYS cc_start: 0.7806 (tptt) cc_final: 0.7432 (mttm)
REVERT: E  219 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8100 (mt-10)
REVERT: A   57 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8226 (mtt90)
REVERT: A   67 PHE cc_start: 0.8449 (m-80) cc_final: 0.8184 (m-10)
REVERT: A  205 SER cc_start: 0.8465 (t) cc_final: 0.8160 (p)
REVERT: A  206 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8327 (tttt)
REVERT: A  220 MET cc_start: 0.8777 (ttp) cc_final: 0.8553 (tmm)
REVERT: A  233 ASN cc_start: 0.5857 (OUTLIER) cc_final: 0.5246 (p0)
REVERT: D  174 ASP cc_start: 0.7478 (m-30) cc_final: 0.7180 (m-30)
REVERT: D  213 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7729 (mt-10)
REVERT: F   19 MET cc_start: 0.7810 (ptp) cc_final: 0.7452 (ptt)
  outliers start: 36
  outliers final: 24
  residues processed: 224
  average time/residue: 0.0997
  time to fit residues: 30.3354
Evaluate side-chains
  221 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN
D 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.122927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095497 restraints weight = 14416.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.099278 restraints weight = 6878.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.101738 restraints weight = 4451.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.103197 restraints weight = 3447.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103939 restraints weight = 2975.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9738  Z= 0.114
  Angle     :  0.515   7.232  13207  Z= 0.260
  Chirality :  0.037   0.140   1593
  Planarity :  0.004   0.049   1673
  Dihedral  :  5.192  60.410   1340
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.62 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.45 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.25), residues: 1235
  helix:  2.42 (0.16), residues: 1052
  sheet:  None (None), residues: 0
  loop : -0.45 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  90 
 TYR   0.008   0.001   TYR F  47 
 PHE   0.008   0.001   PHE G  33 
 TRP   0.005   0.001   TRP E  77 
 HIS   0.008   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9738)
  covalent geometry    : angle       0.51548 (13207)
  hydrogen bonds       : bond        0.03975 (  763)
  hydrogen bonds       : angle       3.72025 ( 2250)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 204
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7643 (ttmt)
REVERT: C  117 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7162 (m-30)
REVERT: B   68 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8441 (ttmm)
REVERT: B   73 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6500 (pm20)
REVERT: B   77 TRP cc_start: 0.8733 (m-10) cc_final: 0.8253 (m-90)
REVERT: B  239 LYS cc_start: 0.9314 (tppt) cc_final: 0.8357 (ttpt)
REVERT: E   64 LYS cc_start: 0.7780 (tptt) cc_final: 0.7391 (mttm)
REVERT: E  219 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8067 (mt-10)
REVERT: A   67 PHE cc_start: 0.8385 (m-80) cc_final: 0.8150 (m-10)
REVERT: A  205 SER cc_start: 0.8358 (t) cc_final: 0.8094 (p)
REVERT: A  218 MET cc_start: 0.8686 (mtt) cc_final: 0.8419 (mtm)
REVERT: A  233 ASN cc_start: 0.5640 (OUTLIER) cc_final: 0.5012 (p0)
REVERT: D  167 GLN cc_start: 0.8144 (tp40) cc_final: 0.7807 (tp40)
REVERT: D  174 ASP cc_start: 0.7495 (m-30) cc_final: 0.7107 (m-30)
REVERT: D  213 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7558 (mt-10)
REVERT: F   19 MET cc_start: 0.7746 (ptp) cc_final: 0.7376 (ptt)
REVERT: F   41 ARG cc_start: 0.6895 (ptp-110) cc_final: 0.6410 (ptp90)
  outliers start: 31
  outliers final: 22
  residues processed: 227
  average time/residue: 0.0903
  time to fit residues: 27.9946
Evaluate side-chains
  216 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 190
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   35 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5628 > 50:
  distance: 4 - 33:  35.668
  distance: 11 - 16:  34.133
  distance: 12 - 47:  35.425
  distance: 16 - 17:  44.139
  distance: 17 - 18:  19.049
  distance: 17 - 20:  34.425
  distance: 18 - 19:   7.181
  distance: 18 - 24:  30.204
  distance: 24 - 25:  40.554
  distance: 25 - 26:  39.534
  distance: 25 - 28:  40.101
  distance: 26 - 33:  39.749
  distance: 27 - 64:   3.339
  distance: 33 - 34:  39.866
  distance: 36 - 72:  39.696
  distance: 38 - 39:  39.989
  distance: 40 - 42:  40.169
  distance: 44 - 46:  13.299
  distance: 45 - 46:  26.768
  distance: 48 - 51:  17.778
  distance: 49 - 55:  13.564
  distance: 51 - 52:  30.471
  distance: 52 - 53:  44.632
  distance: 52 - 54:  42.977
  distance: 55 - 56:  12.370
  distance: 56 - 59:   8.627
  distance: 57 - 58:  37.889
  distance: 58 - 87:  39.225
  distance: 59 - 60:  51.366
  distance: 64 - 65:  10.427
  distance: 65 - 66:  19.350
  distance: 65 - 68:  31.725
  distance: 66 - 67:  38.602
  distance: 66 - 72:   8.472
  distance: 67 - 96:  45.457
  distance: 68 - 69:  24.875
  distance: 69 - 70:  17.557
  distance: 69 - 71:  21.303
  distance: 72 - 73:  48.135
  distance: 73 - 74:  12.203
  distance: 73 - 76:  11.883
  distance: 74 - 75:   5.597
  distance: 74 - 80:  40.539
  distance: 75 - 104:  29.807
  distance: 76 - 77:   6.432
  distance: 77 - 79:  41.301
  distance: 81 - 82:  56.939
  distance: 82 - 83:  39.525
  distance: 82 - 87:  56.780
  distance: 84 - 85:   6.965
  distance: 84 - 86:  57.524
  distance: 87 - 88:  40.466
  distance: 88 - 91:   4.214
  distance: 90 - 116:  33.269
  distance: 91 - 92:  37.009
  distance: 92 - 93:  47.104
  distance: 93 - 95:  33.306
  distance: 96 - 97:  36.610
  distance: 97 - 100:   3.544
  distance: 98 - 104:  35.057
  distance: 99 - 123:  32.578
  distance: 100 - 101:  11.543
  distance: 101 - 102:  27.025
  distance: 102 - 103:  57.066