Starting phenix.real_space_refine on Fri Dec 8 22:18:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2023/6wpw_21866_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2023/6wpw_21866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2023/6wpw_21866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2023/6wpw_21866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2023/6wpw_21866_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpw_21866/12_2023/6wpw_21866_neut.pdb" } resolution = 3.1 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= 0.005 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 56 5.16 5 C 5881 2.51 5 N 1627 2.21 5 O 1698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 380": "NH1" <-> "NH2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "R TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 261": "NH1" <-> "NH2" Residue "R ASP 299": "OD1" <-> "OD2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R ARG 412": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9262 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1835 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2601 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 449 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 244 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3162 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 14, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 5.32, per 1000 atoms: 0.57 Number of scatterers: 9262 At special positions: 0 Unit cell: (167.48, 108.12, 98.58, 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 56 16.00 O 1698 8.00 N 1627 7.00 C 5881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.02 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'C' and resid 11 through 39 removed outlier: 3.554A pdb=" N LYS C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.876A pdb=" N GLU C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.854A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.531A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 4.215A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 353 removed outlier: 4.187A pdb=" N ILE C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 removed outlier: 3.852A pdb=" N ARG C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.552A pdb=" N GLU D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.536A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 removed outlier: 3.665A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.613A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.748A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'R' and resid 27 through 48 removed outlier: 3.503A pdb=" N PHE R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.686A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 removed outlier: 3.842A pdb=" N HIS R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 172 through 197 removed outlier: 3.501A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.552A pdb=" N ARG R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 212 Processing helix chain 'R' and resid 221 through 252 removed outlier: 3.544A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 removed outlier: 3.683A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.632A pdb=" N VAL R 280 " --> pdb=" O MET R 276 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.027A pdb=" N VAL R 285 " --> pdb=" O PRO R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 330 removed outlier: 3.569A pdb=" N ARG R 308 " --> pdb=" O TRP R 304 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.768A pdb=" N ALA R 314 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 335 removed outlier: 4.115A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 removed outlier: 3.596A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 360 through 366 removed outlier: 3.584A pdb=" N PHE R 365 " --> pdb=" O GLU R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 389 removed outlier: 3.621A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 388 " --> pdb=" O PHE R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 removed outlier: 3.648A pdb=" N ALA R 397 " --> pdb=" O GLY R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 423 removed outlier: 3.502A pdb=" N HIS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG R 419 " --> pdb=" O TRP R 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.955A pdb=" N PHE C 212 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.534A pdb=" N VAL C 247 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.720A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 330 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 70 " --> pdb=" O TRP D 82 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.075A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 7.105A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 233 through 234 removed outlier: 3.530A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.640A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.957A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.105A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 77 through 80 removed outlier: 3.516A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1098 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: 2.59 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2946 1.34 - 1.46: 2279 1.46 - 1.58: 4170 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9471 Sorted by residual: bond pdb=" N VAL D 276 " pdb=" CA VAL D 276 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N ILE D 273 " pdb=" CA ILE D 273 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.86e+00 bond pdb=" N VAL D 315 " pdb=" CA VAL D 315 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.79e+00 bond pdb=" N TYR D 289 " pdb=" CA TYR D 289 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.40e+00 bond pdb=" N VAL R 363 " pdb=" CA VAL R 363 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.73e+00 ... (remaining 9466 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.81: 117 104.81 - 112.14: 4471 112.14 - 119.47: 3404 119.47 - 126.79: 4696 126.79 - 134.12: 152 Bond angle restraints: 12840 Sorted by residual: angle pdb=" N PRO R 53 " pdb=" CA PRO R 53 " pdb=" C PRO R 53 " ideal model delta sigma weight residual 112.47 126.57 -14.10 2.06e+00 2.36e-01 4.68e+01 angle pdb=" N LEU R 242 " pdb=" CA LEU R 242 " pdb=" C LEU R 242 " ideal model delta sigma weight residual 111.69 104.42 7.27 1.23e+00 6.61e-01 3.50e+01 angle pdb=" C VAL R 57 " pdb=" N CYS R 58 " pdb=" CA CYS R 58 " ideal model delta sigma weight residual 122.09 112.83 9.26 1.79e+00 3.12e-01 2.67e+01 angle pdb=" C GLY C 353 " pdb=" N ASP C 354 " pdb=" CA ASP C 354 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" N PRO R 53 " pdb=" CA PRO R 53 " pdb=" CB PRO R 53 " ideal model delta sigma weight residual 103.25 98.01 5.24 1.05e+00 9.07e-01 2.49e+01 ... (remaining 12835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 5235 14.82 - 29.65: 292 29.65 - 44.47: 58 44.47 - 59.29: 8 59.29 - 74.12: 4 Dihedral angle restraints: 5597 sinusoidal: 2190 harmonic: 3407 Sorted by residual: dihedral pdb=" CA ASN R 59 " pdb=" C ASN R 59 " pdb=" N ARG R 60 " pdb=" CA ARG R 60 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA CYS R 58 " pdb=" C CYS R 58 " pdb=" N ASN R 59 " pdb=" CA ASN R 59 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 998 0.054 - 0.108: 310 0.108 - 0.163: 92 0.163 - 0.217: 15 0.217 - 0.271: 5 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PRO R 53 " pdb=" N PRO R 53 " pdb=" C PRO R 53 " pdb=" CB PRO R 53 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU R 242 " pdb=" N LEU R 242 " pdb=" C LEU R 242 " pdb=" CB LEU R 242 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1417 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 59 " -0.024 2.00e-02 2.50e+03 1.99e-02 7.95e+00 pdb=" CG TYR D 59 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 59 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 59 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 316 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C LEU R 316 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU R 316 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE R 317 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 318 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ASN R 318 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN R 318 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE R 319 " -0.016 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 13 2.37 - 3.00: 4432 3.00 - 3.63: 13402 3.63 - 4.27: 20910 4.27 - 4.90: 35167 Nonbonded interactions: 73924 Sorted by model distance: nonbonded pdb=" O ILE D 58 " pdb=" OG SER D 316 " model vdw 1.735 2.440 nonbonded pdb=" O GLY D 310 " pdb=" NZ LYS D 337 " model vdw 1.995 2.520 nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 2.204 2.440 nonbonded pdb=" O ASN D 313 " pdb=" OG SER D 331 " model vdw 2.226 2.440 nonbonded pdb=" OG SER D 161 " pdb=" OD1 ASP D 163 " model vdw 2.269 2.440 ... (remaining 73919 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: 0.970 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: 3.590 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.270 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 0.061 9471 Z= 0.434 Angle : 0.950 14.099 12840 Z= 0.553 Chirality : 0.059 0.271 1420 Planarity : 0.007 0.065 1644 Dihedral : 10.181 74.117 3377 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -4.62 (0.20), residues: 1158 helix: -3.85 (0.14), residues: 441 sheet: -2.37 (0.32), residues: 228 loop : -2.40 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 339 HIS 0.016 0.002 HIS C 220 PHE 0.037 0.003 PHE C 238 TYR 0.048 0.003 TYR D 59 ARG 0.008 0.001 ARG D 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.992 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2854 time to fit residues: 74.0938 Evaluate side-chains 147 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 23 ASN C 227 GLN C 357 HIS D 88 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 HIS D 311 HIS N 31 ASN N 82 GLN P 1 HIS ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS R 177 HIS R 238 ASN R 250 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9471 Z= 0.153 Angle : 0.560 6.371 12840 Z= 0.298 Chirality : 0.042 0.163 1420 Planarity : 0.004 0.042 1644 Dihedral : 5.387 40.234 1279 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.42 % Allowed : 8.24 % Favored : 90.34 % 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: -2.70 (0.23), residues: 1158 helix: -1.58 (0.22), residues: 438 sheet: -1.86 (0.32), residues: 228 loop : -1.75 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 25 HIS 0.005 0.001 HIS D 311 PHE 0.013 0.001 PHE R 230 TYR 0.023 0.001 TYR R 145 ARG 0.006 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 190 average time/residue: 0.2769 time to fit residues: 69.2219 Evaluate side-chains 163 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0872 time to fit residues: 2.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 57.2567 > 50: distance: 22 - 202: 25.315 distance: 55 - 206: 9.926 distance: 58 - 203: 26.815 distance: 75 - 188: 19.724 distance: 78 - 185: 19.976 distance: 93 - 169: 13.162 distance: 96 - 166: 26.615 distance: 139 - 146: 4.661 distance: 146 - 147: 8.362 distance: 147 - 148: 28.749 distance: 147 - 150: 30.570 distance: 148 - 149: 20.198 distance: 148 - 154: 22.792 distance: 150 - 151: 31.368 distance: 151 - 152: 11.541 distance: 151 - 153: 7.395 distance: 154 - 155: 18.335 distance: 155 - 156: 36.227 distance: 155 - 158: 34.103 distance: 156 - 157: 36.281 distance: 156 - 161: 30.039 distance: 158 - 159: 21.515 distance: 158 - 160: 34.302 distance: 161 - 162: 12.451 distance: 161 - 298: 21.191 distance: 162 - 163: 31.543 distance: 162 - 165: 28.192 distance: 163 - 164: 32.761 distance: 163 - 166: 25.420 distance: 164 - 295: 32.155 distance: 166 - 167: 10.127 distance: 167 - 168: 31.460 distance: 167 - 170: 24.323 distance: 168 - 169: 17.334 distance: 168 - 173: 32.059 distance: 170 - 171: 13.253 distance: 170 - 172: 9.307 distance: 173 - 174: 35.051 distance: 173 - 282: 19.862 distance: 174 - 175: 42.637 distance: 174 - 177: 27.645 distance: 175 - 176: 9.394 distance: 175 - 185: 41.319 distance: 176 - 279: 13.686 distance: 177 - 178: 15.755 distance: 178 - 179: 11.017 distance: 178 - 180: 12.132 distance: 179 - 181: 13.667 distance: 180 - 182: 10.861 distance: 181 - 183: 11.151 distance: 182 - 183: 16.149 distance: 183 - 184: 11.864 distance: 185 - 186: 34.145 distance: 186 - 187: 41.863 distance: 186 - 189: 32.881 distance: 187 - 188: 22.798 distance: 187 - 197: 39.931 distance: 189 - 190: 7.311 distance: 190 - 191: 9.836 distance: 190 - 192: 9.171 distance: 191 - 193: 19.010 distance: 192 - 194: 33.372 distance: 193 - 195: 29.442 distance: 194 - 195: 22.864 distance: 195 - 196: 17.398 distance: 197 - 198: 19.538 distance: 198 - 199: 8.161 distance: 198 - 201: 21.636 distance: 199 - 200: 24.105 distance: 199 - 203: 12.783 distance: 201 - 202: 16.557 distance: 203 - 204: 30.770 distance: 204 - 205: 18.382 distance: 204 - 207: 11.557 distance: 205 - 206: 19.379 distance: 205 - 208: 17.018 distance: 208 - 209: 22.722 distance: 209 - 210: 25.108 distance: 209 - 212: 18.325 distance: 210 - 211: 29.734 distance: 210 - 219: 24.767 distance: 212 - 213: 4.725 distance: 213 - 214: 30.136 distance: 214 - 215: 5.283 distance: 215 - 216: 18.837 distance: 216 - 217: 23.579 distance: 216 - 218: 22.813 distance: 219 - 220: 11.103 distance: 220 - 221: 8.037 distance: 220 - 223: 26.753 distance: 221 - 222: 13.174 distance: 221 - 225: 25.921 distance: 223 - 224: 14.653 distance: 224 - 242: 17.133