Starting phenix.real_space_refine on Mon Mar 11 14:03:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc3_37429/03_2024/8wc3_37429_neut_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.006 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 59 5.16 5 C 5376 2.51 5 N 1427 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 309": "NH1" <-> "NH2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8418 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1835 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2491 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "R" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1970 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "S" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "Y" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 376 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.94, per 1000 atoms: 0.59 Number of scatterers: 8418 At special positions: 0 Unit cell: (117.3, 96.05, 129.2, 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 59 16.00 O 1556 8.00 N 1427 7.00 C 5376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 14 sheets defined 32.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.925A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.627A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.653A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.832A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 318 removed outlier: 4.229A pdb=" N ARG A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 9 through 25 removed outlier: 4.198A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.237A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 49 removed outlier: 4.033A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 73 removed outlier: 3.876A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY R 72 " --> pdb=" O ASP R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 85 removed outlier: 3.605A pdb=" N ARG R 82 " --> pdb=" O CYS R 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 125 removed outlier: 3.925A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 136 through 159 Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 168 through 173 Processing helix chain 'R' and resid 189 through 220 removed outlier: 5.552A pdb=" N ILE R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 3.619A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 274 Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 300 removed outlier: 4.938A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 11 through 23 removed outlier: 3.509A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 43 removed outlier: 3.919A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'A' and resid 253 through 259 removed outlier: 4.135A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN A 195 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU A 36 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 38 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.907A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.083A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 252 through 254 Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.728A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.519A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.642A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.897A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 174 through 176 342 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1367 1.31 - 1.44: 2457 1.44 - 1.57: 4698 1.57 - 1.70: 1 1.70 - 1.84: 85 Bond restraints: 8608 Sorted by residual: bond pdb=" C6 UJL R 401 " pdb=" C7 UJL R 401 " ideal model delta sigma weight residual 1.607 1.464 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C9 UJL R 401 " pdb=" S1 UJL R 401 " ideal model delta sigma weight residual 1.566 1.708 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C8 UJL R 401 " pdb=" S1 UJL R 401 " ideal model delta sigma weight residual 1.546 1.667 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C LEU R 74 " pdb=" O LEU R 74 " ideal model delta sigma weight residual 1.234 1.188 0.046 8.30e-03 1.45e+04 3.05e+01 bond pdb=" N ILE R 103 " pdb=" CA ILE R 103 " ideal model delta sigma weight residual 1.460 1.395 0.065 1.32e-02 5.74e+03 2.42e+01 ... (remaining 8603 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.37: 306 107.37 - 114.45: 4890 114.45 - 121.53: 4371 121.53 - 128.62: 2076 128.62 - 135.70: 75 Bond angle restraints: 11718 Sorted by residual: angle pdb=" N LYS Y 14 " pdb=" CA LYS Y 14 " pdb=" C LYS Y 14 " ideal model delta sigma weight residual 111.36 123.27 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ILE R 75 " pdb=" CA ILE R 75 " pdb=" C ILE R 75 " ideal model delta sigma weight residual 110.72 120.96 -10.24 1.01e+00 9.80e-01 1.03e+02 angle pdb=" N ALA Y 10 " pdb=" CA ALA Y 10 " pdb=" C ALA Y 10 " ideal model delta sigma weight residual 112.12 124.44 -12.32 1.34e+00 5.57e-01 8.46e+01 angle pdb=" N ALA Y 12 " pdb=" CA ALA Y 12 " pdb=" C ALA Y 12 " ideal model delta sigma weight residual 111.71 102.47 9.24 1.15e+00 7.56e-01 6.45e+01 angle pdb=" N THR S 238 " pdb=" CA THR S 238 " pdb=" C THR S 238 " ideal model delta sigma weight residual 109.96 120.60 -10.64 1.50e+00 4.44e-01 5.03e+01 ... (remaining 11713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4486 16.03 - 32.05: 413 32.05 - 48.08: 105 48.08 - 64.10: 22 64.10 - 80.13: 9 Dihedral angle restraints: 5035 sinusoidal: 1789 harmonic: 3246 Sorted by residual: dihedral pdb=" C TYR S 235 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual -122.60 -150.56 27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual 122.80 149.53 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 43.24 49.76 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 5032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 1333 0.231 - 0.461: 16 0.461 - 0.692: 0 0.692 - 0.922: 0 0.922 - 1.153: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CA ILE R 75 " pdb=" N ILE R 75 " pdb=" C ILE R 75 " pdb=" CB ILE R 75 " both_signs ideal model delta sigma weight residual False 2.43 2.00 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ALA Y 10 " pdb=" N ALA Y 10 " pdb=" C ALA Y 10 " pdb=" CB ALA Y 10 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1347 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 75 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ILE R 75 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE R 75 " 0.027 2.00e-02 2.50e+03 pdb=" N MET R 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 217 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS R 217 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS R 217 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY R 218 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 285 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C TYR A 285 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 285 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 286 " 0.017 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.06: 2 2.06 - 2.77: 1617 2.77 - 3.48: 11136 3.48 - 4.19: 18889 4.19 - 4.90: 33946 Nonbonded interactions: 65590 Sorted by model distance: nonbonded pdb=" NH1 ARG A 352 " pdb=" O ILE R 223 " model vdw 1.356 2.520 nonbonded pdb=" OG SER R 100 " pdb=" CG2 ILE R 158 " model vdw 1.809 3.460 nonbonded pdb=" OG SER B 281 " pdb=" O HIS Y 44 " model vdw 2.232 2.440 nonbonded pdb=" N GLN R 52 " pdb=" OE1 GLN R 52 " model vdw 2.246 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 2.440 ... (remaining 65585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 2.570 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.820 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 : 0.007 0.143 8608 Z= 0.473 Angle : 0.952 12.323 11718 Z= 0.637 Chirality : 0.071 1.153 1350 Planarity : 0.005 0.049 1484 Dihedral : 13.953 80.127 2932 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 2.68 % Favored : 95.93 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1099 helix: 0.21 (0.28), residues: 348 sheet: 0.08 (0.33), residues: 276 loop : -1.91 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 261 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.001 PHE R 289 TYR 0.026 0.001 TYR S 235 ARG 0.007 0.000 ARG R 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.927 Fit side-chains REVERT: S 235 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.5976 (t80) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 1.0980 time to fit residues: 178.6560 Evaluate side-chains 100 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 309 ARG Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 261 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8608 Z= 0.240 Angle : 0.601 8.336 11718 Z= 0.312 Chirality : 0.044 0.277 1350 Planarity : 0.004 0.047 1484 Dihedral : 5.108 49.644 1218 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.73 % Allowed : 11.99 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1099 helix: 1.55 (0.28), residues: 357 sheet: 0.12 (0.33), residues: 272 loop : -1.65 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.002 PHE B 151 TYR 0.034 0.002 TYR S 235 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 0.939 Fit side-chains REVERT: R 294 SER cc_start: 0.7340 (t) cc_final: 0.7026 (m) outliers start: 32 outliers final: 17 residues processed: 117 average time/residue: 1.0576 time to fit residues: 133.3397 Evaluate side-chains 102 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 PHE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8608 Z= 0.267 Angle : 0.603 7.254 11718 Z= 0.315 Chirality : 0.044 0.268 1350 Planarity : 0.004 0.045 1484 Dihedral : 4.663 27.297 1210 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.03 % Allowed : 16.30 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1099 helix: 1.64 (0.28), residues: 356 sheet: 0.08 (0.33), residues: 274 loop : -1.73 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE B 151 TYR 0.034 0.002 TYR S 235 ARG 0.013 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.092 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 1.1069 time to fit residues: 133.1498 Evaluate side-chains 104 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 66.6576 > 50: distance: 51 - 55: 26.300 distance: 55 - 56: 36.850 distance: 56 - 57: 40.494 distance: 56 - 59: 30.493 distance: 57 - 58: 14.259 distance: 57 - 60: 31.072 distance: 60 - 61: 14.072 distance: 61 - 62: 47.832 distance: 61 - 64: 21.611 distance: 62 - 63: 44.573 distance: 62 - 69: 66.324 distance: 64 - 65: 41.849 distance: 65 - 66: 11.434 distance: 66 - 67: 45.767 distance: 67 - 68: 27.168 distance: 69 - 70: 34.325 distance: 70 - 71: 33.516 distance: 70 - 73: 24.709 distance: 71 - 72: 10.148 distance: 71 - 77: 56.478 distance: 73 - 74: 59.219 distance: 73 - 75: 50.443 distance: 74 - 76: 37.229 distance: 77 - 78: 7.528 distance: 78 - 79: 59.721 distance: 78 - 81: 23.796 distance: 79 - 80: 11.389 distance: 79 - 85: 40.412 distance: 81 - 82: 23.461 distance: 82 - 83: 32.398 distance: 82 - 84: 39.765 distance: 85 - 86: 31.283 distance: 86 - 87: 41.332 distance: 86 - 89: 29.123 distance: 87 - 88: 33.618 distance: 87 - 93: 49.530 distance: 88 - 114: 45.891 distance: 89 - 90: 30.352 distance: 89 - 91: 46.943 distance: 90 - 92: 42.739 distance: 93 - 94: 21.781 distance: 94 - 95: 33.381 distance: 94 - 97: 33.205 distance: 95 - 96: 33.562 distance: 95 - 99: 30.974 distance: 96 - 122: 45.808 distance: 97 - 98: 56.875 distance: 99 - 100: 17.123 distance: 100 - 101: 27.164 distance: 100 - 103: 22.447 distance: 101 - 102: 10.606 distance: 101 - 106: 35.496 distance: 102 - 129: 30.410 distance: 103 - 104: 13.361 distance: 103 - 105: 25.523 distance: 106 - 107: 33.336 distance: 107 - 108: 20.379 distance: 107 - 110: 37.971 distance: 108 - 109: 33.756 distance: 108 - 114: 35.457 distance: 109 - 137: 21.490 distance: 110 - 111: 41.077 distance: 110 - 112: 15.142 distance: 111 - 113: 31.468 distance: 114 - 115: 18.772 distance: 115 - 116: 25.274 distance: 115 - 118: 17.303 distance: 116 - 117: 12.768 distance: 116 - 122: 5.624 distance: 117 - 144: 36.695 distance: 118 - 119: 19.771 distance: 119 - 120: 23.602 distance: 119 - 121: 25.316 distance: 122 - 123: 21.578 distance: 123 - 124: 28.859 distance: 123 - 126: 17.126 distance: 124 - 125: 36.279 distance: 124 - 129: 25.129 distance: 125 - 151: 28.690 distance: 126 - 127: 14.407 distance: 126 - 128: 20.788