Starting phenix.real_space_refine on Sat Aug 23 07:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka2_22756/08_2025/7ka2_22756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka2_22756/08_2025/7ka2_22756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ka2_22756/08_2025/7ka2_22756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka2_22756/08_2025/7ka2_22756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ka2_22756/08_2025/7ka2_22756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka2_22756/08_2025/7ka2_22756.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 10472 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Restraints were copied for chains: A, C, D Time building chain proxies: 2.05, per 1000 atoms: 0.20 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 79.17, 106.47, 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 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 0.72 Conformation dependent library (CDL) restraints added in 367.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 55.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.706A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.730A pdb=" N LYS A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.636A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.705A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.538A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.705A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'D' and resid 8 through 24 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.706A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32 removed outlier: 7.121A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 7.121A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 7.120A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 31 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 7.120A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 564 hydrogen bonds defined for protein. 1608 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: 1.25 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3443 1.34 - 1.46: 1851 1.46 - 1.57: 5322 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.92e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.87e+00 bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.77e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.74e+00 bond pdb=" CB GLU B 14 " pdb=" CG GLU B 14 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 13401 1.63 - 3.25: 883 3.25 - 4.88: 115 4.88 - 6.50: 53 6.50 - 8.13: 12 Bond angle restraints: 14464 Sorted by residual: angle pdb=" C ASN D 319 " pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta sigma weight residual 121.19 129.32 -8.13 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C ASN A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta sigma weight residual 121.19 129.31 -8.12 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C ASN B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta sigma weight residual 121.19 129.27 -8.08 1.59e+00 3.96e-01 2.58e+01 angle pdb=" C ASN C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 121.19 129.26 -8.07 1.59e+00 3.96e-01 2.58e+01 angle pdb=" CA GLU C 49 " pdb=" CB GLU C 49 " pdb=" CG GLU C 49 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.47e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 5733 16.52 - 33.03: 591 33.03 - 49.55: 112 49.55 - 66.07: 56 66.07 - 82.58: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA VAL C 264 " pdb=" C VAL C 264 " pdb=" N THR C 265 " pdb=" CA THR C 265 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA VAL A 264 " pdb=" C VAL A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA VAL B 264 " pdb=" C VAL B 264 " pdb=" N THR B 265 " pdb=" CA THR B 265 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1094 0.044 - 0.088: 390 0.088 - 0.133: 116 0.133 - 0.177: 32 0.177 - 0.221: 12 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE B 46 " pdb=" CA ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CG2 ILE B 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE C 46 " pdb=" CA ILE C 46 " pdb=" CG1 ILE C 46 " pdb=" CG2 ILE C 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A 46 " pdb=" CA ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CG2 ILE A 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 329 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS D 329 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS D 329 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG D 330 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS C 329 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 329 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C LYS A 329 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2592 2.78 - 3.31: 9896 3.31 - 3.84: 18124 3.84 - 4.37: 21109 4.37 - 4.90: 35941 Nonbonded interactions: 87662 Sorted by model distance: nonbonded pdb=" O MET D 250 " pdb=" OG1 THR D 254 " model vdw 2.254 3.040 nonbonded pdb=" O MET A 250 " pdb=" OG1 THR A 254 " model vdw 2.254 3.040 nonbonded pdb=" O MET B 250 " pdb=" OG1 THR B 254 " model vdw 2.254 3.040 nonbonded pdb=" O MET C 250 " pdb=" OG1 THR C 254 " model vdw 2.254 3.040 nonbonded pdb=" O THR B 64 " pdb=" OG1 THR B 64 " model vdw 2.259 3.040 ... (remaining 87657 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.008 0.054 10672 Z= 0.353 Angle : 0.961 8.127 14464 Z= 0.549 Chirality : 0.053 0.221 1644 Planarity : 0.008 0.049 1880 Dihedral : 15.204 82.581 3984 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.12 % Allowed : 6.47 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.99 (0.20), residues: 1364 helix: -1.10 (0.16), residues: 672 sheet: -2.01 (0.33), residues: 200 loop : -0.99 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 172 TYR 0.017 0.003 TYR A 213 PHE 0.017 0.003 PHE A 144 TRP 0.022 0.004 TRP B 295 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00797 (10672) covalent geometry : angle 0.96122 (14464) hydrogen bonds : bond 0.16327 ( 564) hydrogen bonds : angle 6.81305 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 334 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.8742 (tpp) cc_final: 0.8428 (tpt) REVERT: A 233 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.6805 (p) REVERT: A 250 MET cc_start: 0.8667 (tpp) cc_final: 0.8419 (tpt) REVERT: A 271 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 301 TYR cc_start: 0.7412 (m-10) cc_final: 0.7003 (m-10) REVERT: C 39 ILE cc_start: 0.9263 (tp) cc_final: 0.8931 (tp) REVERT: C 60 GLN cc_start: 0.8489 (mt0) cc_final: 0.7667 (mt0) REVERT: C 250 MET cc_start: 0.8731 (tpp) cc_final: 0.8468 (tpt) REVERT: C 271 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 301 TYR cc_start: 0.7570 (m-10) cc_final: 0.7022 (m-10) outliers start: 68 outliers final: 6 residues processed: 373 average time/residue: 0.1094 time to fit residues: 55.0415 Evaluate side-chains 195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 60 GLN B 80 HIS B 125 GLN B 168 ASN A 60 GLN A 80 HIS A 125 GLN A 168 ASN C 60 GLN C 80 HIS C 125 GLN D 80 HIS D 168 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072447 restraints weight = 29113.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074807 restraints weight = 16953.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076352 restraints weight = 12059.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077260 restraints weight = 9658.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077915 restraints weight = 8466.205| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.138 Angle : 0.651 8.932 14464 Z= 0.337 Chirality : 0.043 0.170 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.904 28.865 1481 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.33 % Allowed : 14.48 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.22), residues: 1364 helix: 0.79 (0.18), residues: 684 sheet: -1.26 (0.35), residues: 188 loop : -0.49 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 59 TYR 0.019 0.002 TYR C 203 PHE 0.013 0.002 PHE B 93 TRP 0.005 0.001 TRP A 147 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00303 (10672) covalent geometry : angle 0.65111 (14464) hydrogen bonds : bond 0.04446 ( 564) hydrogen bonds : angle 4.54653 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.7807 (tp30) cc_final: 0.7306 (tp30) REVERT: B 229 LYS cc_start: 0.9236 (tttt) cc_final: 0.8939 (tptp) REVERT: B 311 LYS cc_start: 0.9463 (ttpp) cc_final: 0.9227 (ptmm) REVERT: B 316 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8740 (mmtm) REVERT: A 60 GLN cc_start: 0.8845 (mt0) cc_final: 0.8503 (mt0) REVERT: A 82 THR cc_start: 0.9056 (m) cc_final: 0.8795 (m) REVERT: A 250 MET cc_start: 0.8762 (tpp) cc_final: 0.8558 (tpt) REVERT: C 60 GLN cc_start: 0.8754 (mt0) cc_final: 0.8478 (mt0) REVERT: C 82 THR cc_start: 0.9077 (m) cc_final: 0.8850 (m) REVERT: C 250 MET cc_start: 0.8850 (tpp) cc_final: 0.8618 (tpt) REVERT: C 301 TYR cc_start: 0.7500 (m-10) cc_final: 0.7284 (m-10) outliers start: 37 outliers final: 18 residues processed: 259 average time/residue: 0.0838 time to fit residues: 30.9729 Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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 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: 58.2868 > 50: distance: 3 - 24: 7.525 distance: 9 - 35: 19.006 distance: 16 - 43: 8.766 distance: 19 - 24: 8.038 distance: 20 - 50: 6.696 distance: 24 - 25: 11.812 distance: 25 - 26: 18.207 distance: 25 - 28: 14.482 distance: 26 - 27: 9.580 distance: 26 - 35: 37.245 distance: 28 - 29: 21.232 distance: 29 - 30: 7.215 distance: 30 - 31: 9.045 distance: 31 - 32: 8.378 distance: 32 - 33: 8.852 distance: 32 - 34: 7.841 distance: 35 - 36: 12.296 distance: 36 - 37: 22.163 distance: 36 - 39: 11.387 distance: 37 - 38: 15.659 distance: 37 - 43: 16.387 distance: 39 - 40: 23.180 distance: 39 - 41: 33.866 distance: 40 - 42: 8.435 distance: 43 - 44: 8.003 distance: 44 - 45: 10.432 distance: 44 - 47: 16.188 distance: 45 - 46: 3.787 distance: 45 - 50: 4.234 distance: 47 - 48: 9.529 distance: 47 - 49: 13.365 distance: 50 - 51: 8.260 distance: 51 - 52: 19.200 distance: 51 - 54: 10.558 distance: 52 - 53: 13.074 distance: 52 - 55: 6.198 distance: 55 - 56: 18.853 distance: 55 - 61: 11.381 distance: 56 - 57: 3.960 distance: 56 - 59: 20.135 distance: 57 - 58: 11.603 distance: 57 - 62: 17.669 distance: 59 - 60: 20.771 distance: 60 - 61: 11.973 distance: 62 - 63: 13.679 distance: 63 - 64: 4.402 distance: 64 - 65: 7.999 distance: 64 - 66: 12.011 distance: 66 - 67: 5.262 distance: 67 - 68: 10.901 distance: 67 - 70: 17.453 distance: 68 - 69: 21.618 distance: 68 - 75: 9.031 distance: 70 - 71: 22.985 distance: 71 - 72: 17.707 distance: 72 - 73: 12.390 distance: 73 - 74: 32.162 distance: 75 - 76: 11.016 distance: 76 - 77: 5.398 distance: 77 - 78: 12.049 distance: 77 - 79: 13.985 distance: 79 - 177: 14.870 distance: 80 - 81: 3.269 distance: 80 - 83: 4.914 distance: 81 - 87: 6.921 distance: 82 - 190: 14.642 distance: 83 - 84: 16.937 distance: 83 - 85: 16.783 distance: 84 - 86: 36.579 distance: 87 - 88: 8.082 distance: 88 - 89: 4.105 distance: 88 - 91: 4.478 distance: 89 - 90: 12.593 distance: 89 - 95: 5.643 distance: 91 - 92: 14.313 distance: 92 - 93: 11.285 distance: 92 - 94: 7.223