Starting phenix.real_space_refine on Sun Aug 24 11:45:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxh_43617/08_2025/8vxh_43617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxh_43617/08_2025/8vxh_43617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2025/8vxh_43617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2025/8vxh_43617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2025/8vxh_43617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2025/8vxh_43617.map" } resolution = 2.79 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= 0.044 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 6212 2.51 5 N 1692 2.21 5 O 1756 1.98 5 H 9956 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 19668 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4917 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, D Time building chain proxies: 4.52, per 1000 atoms: 0.23 Number of scatterers: 19668 At special positions: 0 Unit cell: (112.35, 112.35, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1756 8.00 N 1692 7.00 C 6212 6.00 H 9956 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 713.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 56.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 134 through 153 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 Processing helix chain 'A' and resid 230 through 262 removed outlier: 3.715A pdb=" N ARG A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 304 removed outlier: 3.710A pdb=" N TYR A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 Processing helix chain 'B' and resid 230 through 262 removed outlier: 3.715A pdb=" N ARG B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 304 removed outlier: 3.711A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 53 through 64 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 134 through 153 Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 Processing helix chain 'C' and resid 230 through 262 removed outlier: 3.714A pdb=" N ARG C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 304 removed outlier: 3.710A pdb=" N TYR C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 79 through 89 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 134 through 153 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'D' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'D' and resid 230 through 262 removed outlier: 3.715A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 304 removed outlier: 3.710A pdb=" N TYR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200 removed outlier: 6.403A pdb=" N VAL A 123 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE A 198 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 125 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL A 200 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 127 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 164 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE A 70 " --> pdb=" O TRP A 41 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 43 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE A 72 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 45 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU A 74 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP A 47 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 71 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL B 313 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 73 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 314 removed outlier: 6.976A pdb=" N LEU D 73 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 313 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 71 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ILE D 70 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 43 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE D 72 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU D 45 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU D 74 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP D 47 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 164 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL D 123 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE D 198 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY D 125 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL D 200 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL D 127 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 200 removed outlier: 6.404A pdb=" N VAL B 123 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 198 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 125 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 200 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL B 127 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 164 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE B 70 " --> pdb=" O TRP B 41 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 43 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 72 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU B 45 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU B 74 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 47 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER B 71 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 313 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 73 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.403A pdb=" N VAL C 123 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE C 198 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 125 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL C 200 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL C 127 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 164 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE C 70 " --> pdb=" O TRP C 41 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 43 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE C 72 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 45 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU C 74 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 71 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL D 313 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 73 " --> pdb=" O GLN D 311 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1716 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: 4.87 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9940 1.03 - 1.23: 16 1.23 - 1.42: 4008 1.42 - 1.61: 5788 1.61 - 1.81: 88 Bond restraints: 19840 Sorted by residual: bond pdb=" CA ILE A 184 " pdb=" CB ILE A 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.76e-01 bond pdb=" CA ILE B 184 " pdb=" CB ILE B 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.64e-01 bond pdb=" CA ILE C 184 " pdb=" CB ILE C 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.42e-01 bond pdb=" CA ILE D 184 " pdb=" CB ILE D 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 5.05e-01 bond pdb=" CA ASP B 48 " pdb=" C ASP B 48 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.14e-02 7.69e+03 4.02e-01 ... (remaining 19835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 32305 0.87 - 1.74: 3398 1.74 - 2.61: 149 2.61 - 3.49: 48 3.49 - 4.36: 20 Bond angle restraints: 35920 Sorted by residual: angle pdb=" C GLU A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta sigma weight residual 120.33 122.74 -2.41 8.00e-01 1.56e+00 9.06e+00 angle pdb=" C GLU B 109 " pdb=" N ILE B 110 " pdb=" CA ILE B 110 " ideal model delta sigma weight residual 120.33 122.73 -2.40 8.00e-01 1.56e+00 8.97e+00 angle pdb=" C GLU C 109 " pdb=" N ILE C 110 " pdb=" CA ILE C 110 " ideal model delta sigma weight residual 120.33 122.72 -2.39 8.00e-01 1.56e+00 8.91e+00 angle pdb=" C GLU D 109 " pdb=" N ILE D 110 " pdb=" CA ILE D 110 " ideal model delta sigma weight residual 120.33 122.71 -2.38 8.00e-01 1.56e+00 8.87e+00 angle pdb=" C ILE A 110 " pdb=" CA ILE A 110 " pdb=" CB ILE A 110 " ideal model delta sigma weight residual 114.00 110.87 3.13 1.31e+00 5.83e-01 5.71e+00 ... (remaining 35915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 8657 16.13 - 32.26: 347 32.26 - 48.40: 151 48.40 - 64.53: 101 64.53 - 80.66: 8 Dihedral angle restraints: 9264 sinusoidal: 5128 harmonic: 4136 Sorted by residual: dihedral pdb=" CA ARG A 303 " pdb=" C ARG A 303 " pdb=" N ALA A 304 " pdb=" CA ALA A 304 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ARG B 303 " pdb=" C ARG B 303 " pdb=" N ALA B 304 " pdb=" CA ALA B 304 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ARG D 303 " pdb=" C ARG D 303 " pdb=" N ALA D 304 " pdb=" CA ALA D 304 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 9261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 982 0.025 - 0.051: 322 0.051 - 0.076: 156 0.076 - 0.102: 42 0.102 - 0.127: 78 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA ILE B 70 " pdb=" N ILE B 70 " pdb=" C ILE B 70 " pdb=" CB ILE B 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE D 70 " pdb=" N ILE D 70 " pdb=" C ILE D 70 " pdb=" CB ILE D 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1577 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 106 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO A 107 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 106 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO B 107 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 106 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO D 107 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " -0.015 5.00e-02 4.00e+02 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1319 2.22 - 2.81: 41355 2.81 - 3.41: 51167 3.41 - 4.00: 68161 4.00 - 4.60: 106876 Nonbonded interactions: 268878 Sorted by model distance: nonbonded pdb=" O MET A 215 " pdb="HD21 ASN A 219 " model vdw 1.622 2.450 nonbonded pdb=" O MET D 215 " pdb="HD21 ASN D 219 " model vdw 1.622 2.450 nonbonded pdb=" O MET C 215 " pdb="HD21 ASN C 219 " model vdw 1.622 2.450 nonbonded pdb=" O MET B 215 " pdb="HD21 ASN B 219 " model vdw 1.623 2.450 nonbonded pdb=" OD1 ASP B 223 " pdb="HH21 ARG C 297 " model vdw 1.649 2.450 ... (remaining 268873 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 21.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9884 Z= 0.109 Angle : 0.462 4.356 13392 Z= 0.270 Chirality : 0.040 0.127 1580 Planarity : 0.003 0.026 1704 Dihedral : 9.660 80.662 3660 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.14 (0.25), residues: 1232 helix: 3.42 (0.21), residues: 676 sheet: 2.12 (0.39), residues: 204 loop : -0.85 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 297 TYR 0.007 0.001 TYR A 299 PHE 0.006 0.001 PHE D 183 TRP 0.002 0.000 TRP D 41 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9884) covalent geometry : angle 0.46179 (13392) hydrogen bonds : bond 0.13551 ( 576) hydrogen bonds : angle 6.03222 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6687 (tt0) cc_final: 0.6423 (mt-10) REVERT: A 122 ASP cc_start: 0.8922 (m-30) cc_final: 0.8702 (m-30) REVERT: A 149 GLN cc_start: 0.7414 (tt0) cc_final: 0.7090 (tp40) REVERT: A 221 MET cc_start: 0.7337 (mmp) cc_final: 0.6497 (tmt) REVERT: A 255 ILE cc_start: 0.8140 (mm) cc_final: 0.7892 (mp) REVERT: B 64 GLU cc_start: 0.6638 (tt0) cc_final: 0.6379 (mt-10) REVERT: B 149 GLN cc_start: 0.7354 (tt0) cc_final: 0.7092 (tp40) REVERT: B 221 MET cc_start: 0.7292 (mmp) cc_final: 0.6413 (tmt) REVERT: C 122 ASP cc_start: 0.8944 (m-30) cc_final: 0.8651 (m-30) REVERT: C 149 GLN cc_start: 0.7353 (tt0) cc_final: 0.7047 (tp40) REVERT: C 221 MET cc_start: 0.7312 (mmp) cc_final: 0.6462 (tmt) REVERT: D 64 GLU cc_start: 0.6609 (tt0) cc_final: 0.6362 (mt-10) REVERT: D 122 ASP cc_start: 0.8924 (m-30) cc_final: 0.8638 (m-30) REVERT: D 149 GLN cc_start: 0.7386 (tt0) cc_final: 0.7084 (tp40) REVERT: D 221 MET cc_start: 0.7364 (mmp) cc_final: 0.6504 (tmt) REVERT: D 255 ILE cc_start: 0.8104 (mm) cc_final: 0.7903 (mp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 1.1369 time to fit residues: 270.0189 Evaluate side-chains 162 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 132 GLN B 130 ASN B 132 GLN C 130 ASN C 132 GLN D 130 ASN D 132 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117091 restraints weight = 31375.386| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.90 r_work: 0.3284 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9884 Z= 0.151 Angle : 0.507 4.559 13392 Z= 0.272 Chirality : 0.044 0.152 1580 Planarity : 0.005 0.031 1704 Dihedral : 3.814 24.557 1368 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.24 % Allowed : 5.63 % Favored : 93.13 % 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: 2.47 (0.24), residues: 1232 helix: 2.86 (0.20), residues: 688 sheet: 2.32 (0.40), residues: 168 loop : -1.20 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.007 0.001 TYR C 166 PHE 0.008 0.001 PHE B 88 TRP 0.004 0.001 TRP A 41 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9884) covalent geometry : angle 0.50659 (13392) hydrogen bonds : bond 0.06114 ( 576) hydrogen bonds : angle 4.74880 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7436 (pttt) REVERT: A 64 GLU cc_start: 0.6895 (tt0) cc_final: 0.6455 (mt-10) REVERT: A 122 ASP cc_start: 0.9091 (m-30) cc_final: 0.8808 (m-30) REVERT: A 149 GLN cc_start: 0.7269 (tt0) cc_final: 0.6808 (tp40) REVERT: A 221 MET cc_start: 0.7450 (mmp) cc_final: 0.6457 (tmt) REVERT: A 251 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 8 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7353 (pttt) REVERT: B 64 GLU cc_start: 0.6897 (tt0) cc_final: 0.6450 (mt-10) REVERT: B 122 ASP cc_start: 0.9077 (m-30) cc_final: 0.8864 (m-30) REVERT: B 149 GLN cc_start: 0.7129 (tt0) cc_final: 0.6697 (tp40) REVERT: B 221 MET cc_start: 0.7559 (mmp) cc_final: 0.6600 (tmt) REVERT: B 251 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7965 (m) REVERT: C 8 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7415 (pttt) REVERT: C 142 LYS cc_start: 0.7363 (mptm) cc_final: 0.7130 (mptm) REVERT: C 149 GLN cc_start: 0.7231 (tt0) cc_final: 0.6755 (tp40) REVERT: C 215 MET cc_start: 0.6020 (mmp) cc_final: 0.5726 (mmt) REVERT: C 221 MET cc_start: 0.7498 (mmp) cc_final: 0.6535 (tmt) REVERT: C 251 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7976 (m) REVERT: D 8 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7381 (pttt) REVERT: D 64 GLU cc_start: 0.6898 (tt0) cc_final: 0.6456 (mt-10) REVERT: D 149 GLN cc_start: 0.7226 (tt0) cc_final: 0.6792 (tp40) REVERT: D 221 MET cc_start: 0.7459 (mmp) cc_final: 0.6465 (tmt) REVERT: D 251 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7988 (m) outliers start: 13 outliers final: 4 residues processed: 162 average time/residue: 0.9484 time to fit residues: 167.7075 Evaluate side-chains 168 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER 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: 63.9499 > 50: distance: 107 - 385: 16.506 distance: 175 - 191: 3.346 distance: 293 - 304: 13.523 distance: 304 - 315: 9.416 distance: 305 - 306: 27.727 distance: 305 - 308: 13.453 distance: 305 - 316: 18.778 distance: 306 - 307: 27.841 distance: 306 - 328: 24.442 distance: 308 - 309: 13.018 distance: 308 - 317: 23.474 distance: 308 - 318: 23.771 distance: 309 - 310: 8.969 distance: 309 - 319: 20.096 distance: 309 - 320: 13.498 distance: 310 - 311: 14.141 distance: 310 - 321: 4.578 distance: 310 - 322: 10.476 distance: 311 - 312: 21.771 distance: 311 - 323: 8.590 distance: 312 - 313: 20.068 distance: 312 - 314: 15.219 distance: 313 - 324: 8.057 distance: 313 - 325: 11.831 distance: 314 - 326: 4.794 distance: 314 - 327: 7.791 distance: 328 - 329: 22.523 distance: 328 - 340: 12.483 distance: 329 - 330: 32.392 distance: 329 - 332: 23.527 distance: 329 - 341: 14.082 distance: 330 - 331: 30.028 distance: 330 - 349: 23.732 distance: 332 - 333: 20.420 distance: 332 - 342: 15.614 distance: 332 - 343: 13.525 distance: 333 - 334: 12.577 distance: 333 - 335: 6.640 distance: 334 - 336: 7.430 distance: 334 - 344: 7.292 distance: 335 - 337: 7.182 distance: 335 - 345: 11.674 distance: 336 - 338: 11.222 distance: 336 - 346: 3.863 distance: 337 - 338: 8.135 distance: 337 - 347: 4.549 distance: 338 - 339: 5.569 distance: 339 - 348: 5.028 distance: 349 - 350: 23.727 distance: 349 - 360: 22.743 distance: 350 - 351: 33.056 distance: 350 - 353: 22.292 distance: 350 - 361: 14.919 distance: 351 - 352: 28.567 distance: 351 - 369: 13.599 distance: 353 - 354: 16.221 distance: 353 - 362: 31.152 distance: 353 - 363: 25.717 distance: 354 - 355: 6.347 distance: 354 - 356: 12.310 distance: 355 - 357: 5.669 distance: 355 - 364: 10.296 distance: 356 - 358: 8.542 distance: 356 - 365: 7.181 distance: 357 - 359: 5.868 distance: 357 - 366: 10.334 distance: 358 - 359: 12.806 distance: 358 - 367: 3.669 distance: 359 - 368: 15.464 distance: 369 - 370: 23.578 distance: 369 - 376: 46.030 distance: 370 - 371: 48.547 distance: 370 - 373: 43.423 distance: 370 - 377: 16.723 distance: 371 - 372: 49.743 distance: 371 - 385: 44.400 distance: 373 - 374: 31.585 distance: 373 - 375: 27.772 distance: 373 - 378: 11.089 distance: 374 - 379: 13.725 distance: 374 - 380: 8.745 distance: 374 - 381: 20.500 distance: 375 - 382: 17.676 distance: 375 - 383: 13.667 distance: 375 - 384: 20.735 distance: 385 - 386: 44.062 distance: 385 - 394: 33.403 distance: 386 - 387: 42.571 distance: 386 - 389: 10.794 distance: 386 - 395: 40.413 distance: 387 - 388: 21.262 distance: 387 - 402: 24.549 distance: 389 - 390: 14.292 distance: 389 - 396: 18.481 distance: 389 - 397: 32.111 distance: 390 - 391: 12.775 distance: 390 - 398: 28.090 distance: 390 - 399: 11.344 distance: 391 - 392: 11.542 distance: 391 - 393: 10.858 distance: 393 - 400: 17.888 distance: 393 - 401: 7.166 distance: 402 - 403: 11.302 distance: 402 - 411: 13.793 distance: 403 - 404: 17.478 distance: 403 - 406: 9.232 distance: 403 - 412: 14.247 distance: 404 - 405: 22.410 distance: 404 - 419: 11.404 distance: 406 - 407: 9.366 distance: 406 - 413: 11.919 distance: 406 - 414: 13.242 distance: 407 - 408: 7.718 distance: 407 - 415: 10.734 distance: 407 - 416: 10.313 distance: 408 - 409: 4.634 distance: 408 - 410: 8.167 distance: 410 - 417: 12.897 distance: 410 - 418: 13.292 distance: 419 - 420: 26.383 distance: 419 - 426: 16.220 distance: 420 - 421: 47.043 distance: 420 - 423: 30.459 distance: 420 - 427: 28.837 distance: 421 - 422: 25.524 distance: 421 - 435: 17.811 distance: 423 - 424: 15.787 distance: 423 - 425: 7.579 distance: 423 - 428: 17.801 distance: 424 - 429: 11.417 distance: 424 - 431: 8.916 distance: 425 - 432: 15.228 distance: 425 - 433: 13.096 distance: 425 - 434: 10.940 distance: 435 - 436: 35.599 distance: 435 - 443: 9.136 distance: 436 - 437: 27.802 distance: 436 - 439: 22.849 distance: 436 - 444: 17.956 distance: 437 - 438: 56.698 distance: 437 - 454: 12.571 distance: 439 - 440: 18.940 distance: 439 - 441: 22.849 distance: 439 - 445: 27.631 distance: 440 - 442: 14.376 distance: 440 - 446: 14.786 distance: 440 - 447: 14.890 distance: 441 - 448: 10.129 distance: 441 - 449: 9.957 distance: 441 - 450: 6.086 distance: 442 - 451: 15.637 distance: 442 - 452: 9.788 distance: 442 - 453: 14.491 distance: 454 - 455: 26.513 distance: 454 - 466: 40.365 distance: 455 - 456: 60.075 distance: 455 - 458: 43.930 distance: 455 - 467: 29.076 distance: 456 - 457: 57.229 distance: 456 - 475: 33.860 distance: 458 - 459: 19.362 distance: 458 - 468: 13.346 distance: 458 - 469: 23.345 distance: 459 - 460: 11.337 distance: 459 - 461: 16.631 distance: 460 - 462: 8.127 distance: 460 - 470: 8.338 distance: 461 - 463: 14.147 distance: 461 - 471: 8.505 distance: 462 - 464: 4.219 distance: 462 - 472: 8.346 distance: 463 - 464: 7.146 distance: 463 - 473: 8.181 distance: 464 - 465: 12.557 distance: 465 - 474: 14.703 distance: 475 - 476: 7.840 distance: 475 - 481: 20.902 distance: 476 - 477: 33.793 distance: 476 - 479: 25.260 distance: 476 - 482: 15.241 distance: 477 - 478: 32.788 distance: 477 - 489: 28.991 distance: 479 - 480: 35.725 distance: 479 - 483: 25.876 distance: 479 - 484: 22.058 distance: 480 - 481: 27.108 distance: 480 - 485: 16.168 distance: 480 - 486: 16.088 distance: 481 - 487: 34.859 distance: 481 - 488: 27.494