Starting phenix.real_space_refine on Sat Aug 3 20:13:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uru_42501/08_2024/8uru_42501.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uru_42501/08_2024/8uru_42501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uru_42501/08_2024/8uru_42501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uru_42501/08_2024/8uru_42501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uru_42501/08_2024/8uru_42501.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uru_42501/08_2024/8uru_42501.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 5555 2.51 5 N 1517 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "F GLU 25": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2913 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 347} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1860 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain breaks: 4 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2822 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 882 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8895 At special positions: 0 Unit cell: (110.656, 111.72, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 43 15.00 Mg 1 11.99 O 1742 8.00 N 1517 7.00 C 5555 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 - 3.50 Amino acid : False - 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: 3.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 28.5% alpha, 12.8% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.651A pdb=" N SER A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 122 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.623A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.691A pdb=" N PHE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.044A pdb=" N VAL A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 5.288A pdb=" N ASN A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 320 through 328 removed outlier: 6.174A pdb=" N LEU A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.607A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 134 removed outlier: 4.393A pdb=" N LEU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 134' Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.968A pdb=" N TYR B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.930A pdb=" N ILE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.848A pdb=" N ALA B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.588A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.576A pdb=" N ASP C 335 " --> pdb=" O HIS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.662A pdb=" N LEU F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 20 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 32 removed outlier: 4.145A pdb=" N GLN F 30 " --> pdb=" O ARG F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.545A pdb=" N THR F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN F 58 " --> pdb=" O MET F 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.953A pdb=" N ARG A 25 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 70 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 27 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLN A 72 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.409A pdb=" N THR A 128 " --> pdb=" O ILE A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5 removed outlier: 4.337A pdb=" N ARG B 35 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 49 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU B 148 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 4.037A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.512A pdb=" N LEU C 38 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 40 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 56 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.557A pdb=" N LEU C 83 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N CYS C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 130 removed outlier: 3.742A pdb=" N ALA C 126 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 141 " --> pdb=" O TRP C 153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 151 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.510A pdb=" N ILE C 200 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 210 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 250 through 254 removed outlier: 3.507A pdb=" N CYS C 259 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 260 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 296 removed outlier: 6.682A pdb=" N ALA C 309 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 316 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY C 310 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 315 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 328 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE C 317 " --> pdb=" O ILE C 326 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1379 1.32 - 1.44: 2675 1.44 - 1.57: 4967 1.57 - 1.70: 84 1.70 - 1.83: 54 Bond restraints: 9159 Sorted by residual: bond pdb=" CA PHE A 91 " pdb=" C PHE A 91 " ideal model delta sigma weight residual 1.525 1.483 0.042 1.07e-02 8.73e+03 1.51e+01 bond pdb=" C LEU A 175 " pdb=" O LEU A 175 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.28e-02 6.10e+03 1.14e+01 bond pdb=" C PHE A 91 " pdb=" O PHE A 91 " ideal model delta sigma weight residual 1.245 1.198 0.047 1.53e-02 4.27e+03 9.58e+00 bond pdb=" CA ASP A 90 " pdb=" C ASP A 90 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.37e-02 5.33e+03 8.95e+00 bond pdb=" CA LEU B 221 " pdb=" C LEU B 221 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.26e-02 6.30e+03 7.94e+00 ... (remaining 9154 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.78: 482 106.78 - 114.29: 5312 114.29 - 121.79: 4691 121.79 - 129.29: 1981 129.29 - 136.79: 87 Bond angle restraints: 12553 Sorted by residual: angle pdb=" C TYR B 188 " pdb=" N PRO B 189 " pdb=" CA PRO B 189 " ideal model delta sigma weight residual 119.84 131.45 -11.61 1.25e+00 6.40e-01 8.62e+01 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 110.97 123.31 -12.34 1.56e+00 4.11e-01 6.26e+01 angle pdb=" N ALA A 171 " pdb=" CA ALA A 171 " pdb=" C ALA A 171 " ideal model delta sigma weight residual 113.19 121.97 -8.78 1.19e+00 7.06e-01 5.44e+01 angle pdb=" N SER B 196 " pdb=" CA SER B 196 " pdb=" C SER B 196 " ideal model delta sigma weight residual 112.93 104.56 8.37 1.33e+00 5.65e-01 3.96e+01 angle pdb=" C ILE A 353 " pdb=" CA ILE A 353 " pdb=" CB ILE A 353 " ideal model delta sigma weight residual 111.06 105.69 5.37 8.80e-01 1.29e+00 3.72e+01 ... (remaining 12548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4200 17.88 - 35.76: 790 35.76 - 53.64: 312 53.64 - 71.51: 68 71.51 - 89.39: 10 Dihedral angle restraints: 5380 sinusoidal: 2451 harmonic: 2929 Sorted by residual: dihedral pdb=" CA SER B 218 " pdb=" C SER B 218 " pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual 180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CA GLN A 172 " pdb=" CB GLN A 172 " ideal model delta harmonic sigma weight residual 122.80 133.33 -10.53 0 2.50e+00 1.60e-01 1.77e+01 ... (remaining 5377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1318 0.086 - 0.172: 98 0.172 - 0.258: 13 0.258 - 0.344: 2 0.344 - 0.431: 2 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA GLN A 172 " pdb=" N GLN A 172 " pdb=" C GLN A 172 " pdb=" CB GLN A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU B 221 " pdb=" N LEU B 221 " pdb=" C LEU B 221 " pdb=" CB LEU B 221 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1430 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 91 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C GLY C 91 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY C 91 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP C 92 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 242 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO C 243 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 77 " 0.025 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE B 77 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 77 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 77 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 77 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 77 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 142 2.63 - 3.19: 7855 3.19 - 3.76: 13789 3.76 - 4.33: 18078 4.33 - 4.90: 28991 Nonbonded interactions: 68855 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb="MG MG A 501 " model vdw 2.058 2.170 nonbonded pdb=" OD2 ASP A 290 " pdb="MG MG A 501 " model vdw 2.122 2.170 nonbonded pdb=" O ILE B 165 " pdb=" OG SER B 166 " model vdw 2.183 3.040 nonbonded pdb=" N GLN F 30 " pdb=" OE1 GLN F 30 " model vdw 2.217 3.120 nonbonded pdb=" O LYS A 173 " pdb=" NZ LYS A 173 " model vdw 2.221 3.120 ... (remaining 68850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.800 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.005 0.064 9159 Z= 0.299 Angle : 0.979 13.421 12553 Z= 0.565 Chirality : 0.050 0.431 1433 Planarity : 0.006 0.068 1426 Dihedral : 21.437 89.392 3460 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.95 % Favored : 88.11 % Rotamer: Outliers : 3.21 % Allowed : 33.22 % Favored : 63.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.25), residues: 959 helix: -0.16 (0.34), residues: 244 sheet: -2.19 (0.37), residues: 176 loop : -2.88 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 41 HIS 0.011 0.001 HIS C 15 PHE 0.041 0.002 PHE B 77 TYR 0.014 0.001 TYR A 275 ARG 0.007 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7707 (mtpt) REVERT: A 378 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 47 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7633 (pp) REVERT: B 82 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6861 (pt0) REVERT: B 184 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 192 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: B 221 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7131 (tt) REVERT: C 53 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7110 (p0) outliers start: 29 outliers final: 16 residues processed: 165 average time/residue: 0.2238 time to fit residues: 49.7769 Evaluate side-chains 143 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 45 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 122 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 0.0060 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN F 20 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9159 Z= 0.207 Angle : 0.706 9.002 12553 Z= 0.366 Chirality : 0.044 0.255 1433 Planarity : 0.005 0.062 1426 Dihedral : 19.570 84.393 1569 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.70 % Favored : 89.68 % Rotamer: Outliers : 6.20 % Allowed : 27.91 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.26), residues: 959 helix: 0.33 (0.33), residues: 244 sheet: -2.07 (0.37), residues: 168 loop : -2.54 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.008 0.001 HIS C 15 PHE 0.019 0.002 PHE B 11 TYR 0.012 0.001 TYR A 275 ARG 0.005 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 141 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8241 (mt) cc_final: 0.7703 (mp) REVERT: B 47 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7492 (pp) REVERT: B 82 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6683 (pt0) REVERT: C 53 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7662 (p0) REVERT: C 173 LEU cc_start: 0.7772 (tp) cc_final: 0.7455 (tp) REVERT: F 25 GLU cc_start: 0.7906 (tp30) cc_final: 0.7628 (tp30) outliers start: 56 outliers final: 29 residues processed: 183 average time/residue: 0.2016 time to fit residues: 51.0899 Evaluate side-chains 155 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 382 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9159 Z= 0.258 Angle : 0.700 8.862 12553 Z= 0.362 Chirality : 0.044 0.279 1433 Planarity : 0.005 0.058 1426 Dihedral : 19.291 84.372 1542 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.11 % Favored : 89.47 % Rotamer: Outliers : 6.09 % Allowed : 29.35 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.26), residues: 959 helix: 0.39 (0.34), residues: 248 sheet: -1.92 (0.37), residues: 174 loop : -2.46 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 293 HIS 0.007 0.001 HIS C 66 PHE 0.016 0.002 PHE B 77 TYR 0.013 0.001 TYR A 275 ARG 0.007 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 140 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8279 (mt) cc_final: 0.8055 (mt) REVERT: A 387 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6498 (tmm) REVERT: B 47 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7404 (pp) REVERT: B 82 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6854 (pt0) REVERT: C 52 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.7059 (mmtm) REVERT: C 183 MET cc_start: 0.6140 (tmm) cc_final: 0.5937 (tmm) REVERT: C 362 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7921 (m-10) outliers start: 55 outliers final: 28 residues processed: 181 average time/residue: 0.2282 time to fit residues: 55.7667 Evaluate side-chains 158 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 362 PHE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain F residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1913 > 50: distance: 63 - 186: 10.597 distance: 72 - 177: 14.021 distance: 75 - 174: 9.290 distance: 89 - 163: 18.664 distance: 92 - 160: 16.223 distance: 124 - 127: 3.478 distance: 127 - 128: 22.198 distance: 128 - 129: 33.234 distance: 128 - 131: 6.698 distance: 129 - 130: 26.096 distance: 129 - 135: 20.491 distance: 131 - 132: 17.473 distance: 132 - 133: 7.786 distance: 132 - 134: 11.295 distance: 135 - 136: 9.910 distance: 136 - 137: 26.533 distance: 136 - 139: 14.421 distance: 137 - 138: 20.953 distance: 137 - 143: 19.573 distance: 140 - 141: 3.877 distance: 140 - 142: 34.270 distance: 143 - 144: 17.027 distance: 144 - 145: 10.639 distance: 144 - 147: 17.364 distance: 145 - 146: 22.251 distance: 145 - 151: 9.044 distance: 147 - 148: 24.188 distance: 148 - 149: 14.372 distance: 148 - 150: 14.129 distance: 151 - 152: 7.234 distance: 152 - 153: 5.132 distance: 152 - 155: 11.846 distance: 153 - 154: 30.934 distance: 153 - 160: 17.936 distance: 155 - 156: 8.835 distance: 156 - 157: 10.145 distance: 157 - 158: 9.295 distance: 157 - 159: 11.903 distance: 160 - 161: 8.722 distance: 161 - 162: 9.414 distance: 161 - 164: 11.560 distance: 162 - 166: 7.505 distance: 164 - 165: 16.984 distance: 166 - 167: 12.447 distance: 166 - 247: 22.551 distance: 167 - 168: 4.979 distance: 167 - 170: 12.902 distance: 168 - 169: 6.506 distance: 168 - 174: 4.715 distance: 169 - 244: 6.644 distance: 170 - 171: 10.692 distance: 171 - 172: 10.111 distance: 171 - 173: 9.259 distance: 174 - 175: 6.140 distance: 175 - 176: 8.227 distance: 175 - 178: 10.986 distance: 176 - 177: 8.265 distance: 176 - 180: 7.389 distance: 178 - 179: 39.088 distance: 180 - 181: 26.830 distance: 180 - 226: 16.166 distance: 181 - 182: 17.633 distance: 181 - 184: 25.771 distance: 182 - 183: 9.781 distance: 182 - 186: 8.314 distance: 183 - 223: 17.189 distance: 184 - 185: 40.420 distance: 186 - 187: 11.084 distance: 187 - 188: 21.437 distance: 187 - 190: 18.183 distance: 188 - 189: 33.627 distance: 188 - 193: 16.823 distance: 190 - 191: 12.211 distance: 190 - 192: 15.560 distance: 193 - 194: 8.866 distance: 194 - 195: 30.964 distance: 194 - 197: 8.581 distance: 195 - 196: 15.401 distance: 195 - 199: 28.546 distance: 197 - 198: 22.698