Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 3 13:26:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/05_2023/6irs_9721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/05_2023/6irs_9721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/05_2023/6irs_9721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/05_2023/6irs_9721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/05_2023/6irs_9721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/05_2023/6irs_9721_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4807 2.51 5 N 1172 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 7337 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3479 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.62 Number of scatterers: 7337 At special positions: 0 Unit cell: (82.916, 84.007, 124.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1329 8.00 N 1172 7.00 C 4807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 5 sheets defined 51.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.677A pdb=" N LEU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 222 removed outlier: 3.863A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.985A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.631A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 341 removed outlier: 4.212A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.717A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.837A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 392' Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.530A pdb=" N THR A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 3.921A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.619A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.908A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 69 removed outlier: 3.554A pdb=" N PHE B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.760A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 109 removed outlier: 3.553A pdb=" N PHE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.638A pdb=" N TYR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 122 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.542A pdb=" N GLU B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.860A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 187 removed outlier: 4.036A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 220 removed outlier: 3.848A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.721A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 274 through 299 removed outlier: 3.698A pdb=" N ILE B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 4.205A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.817A pdb=" N LEU B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.855A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 347 through 355 removed outlier: 3.563A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.510A pdb=" N MET B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 420 removed outlier: 3.619A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.841A pdb=" N VAL B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 467 through 473 removed outlier: 4.007A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.656A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 259 through 262 removed outlier: 6.928A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.514A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 624 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.986A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 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: 1.20 - 1.33: 1456 1.33 - 1.45: 1777 1.45 - 1.57: 4235 1.57 - 1.69: 4 1.69 - 1.81: 40 Bond restraints: 7512 Sorted by residual: bond pdb=" C31 3PH B 601 " pdb=" O31 3PH B 601 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.452 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C21 3PH B 601 " pdb=" O21 3PH B 601 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.632 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.53: 108 103.53 - 111.31: 3194 111.31 - 119.09: 3000 119.09 - 126.86: 3780 126.86 - 134.64: 128 Bond angle restraints: 10210 Sorted by residual: angle pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 129.79 -9.95 1.25e+00 6.40e-01 6.34e+01 angle pdb=" N MET A 490 " pdb=" CA MET A 490 " pdb=" C MET A 490 " ideal model delta sigma weight residual 109.15 97.87 11.28 1.44e+00 4.82e-01 6.14e+01 angle pdb=" N MET A 508 " pdb=" CA MET A 508 " pdb=" C MET A 508 " ideal model delta sigma weight residual 111.28 118.86 -7.58 1.09e+00 8.42e-01 4.84e+01 angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" C PHE B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta sigma weight residual 119.84 127.10 -7.26 1.25e+00 6.40e-01 3.38e+01 ... (remaining 10205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4057 17.73 - 35.46: 217 35.46 - 53.19: 62 53.19 - 70.92: 11 70.92 - 88.65: 3 Dihedral angle restraints: 4350 sinusoidal: 1697 harmonic: 2653 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 -178.35 -88.65 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CA PRO B 360 " pdb=" C PRO B 360 " pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS A 221 " pdb=" C HIS A 221 " pdb=" N THR A 222 " pdb=" CA THR A 222 " ideal model delta harmonic sigma weight residual 180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 983 0.081 - 0.162: 184 0.162 - 0.242: 23 0.242 - 0.323: 6 0.323 - 0.404: 4 Chirality restraints: 1200 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.17e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1197 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG D 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.321 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG D 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 507 " -0.090 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN A 507 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 507 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 507 " 0.196 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.133 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 403 2.70 - 3.25: 7108 3.25 - 3.80: 11590 3.80 - 4.35: 14642 4.35 - 4.90: 23870 Nonbonded interactions: 57613 Sorted by model distance: nonbonded pdb=" ND1 HIS B 367 " pdb=" CD PRO B 368 " model vdw 2.150 3.520 nonbonded pdb=" O GLY B 107 " pdb=" OG SER B 111 " model vdw 2.199 2.440 nonbonded pdb=" C TRP A 492 " pdb=" CG2 THR A 509 " model vdw 2.221 3.690 nonbonded pdb=" CD1 ILE A 228 " pdb=" CZ PHE A 234 " model vdw 2.250 3.760 nonbonded pdb=" O CYS B 92 " pdb=" OH TYR B 254 " model vdw 2.277 2.440 ... (remaining 57608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.690 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: 4.210 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.300 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.011 0.129 7512 Z= 0.710 Angle : 1.357 12.491 10210 Z= 0.743 Chirality : 0.069 0.404 1200 Planarity : 0.014 0.287 1254 Dihedral : 12.692 77.395 2643 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.79 % Favored : 90.35 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -5.69 (0.19), residues: 922 helix: -4.10 (0.12), residues: 475 sheet: -1.86 (0.67), residues: 51 loop : -3.48 (0.25), residues: 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 7 residues processed: 238 average time/residue: 0.2153 time to fit residues: 66.4050 Evaluate side-chains 139 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0764 time to fit residues: 2.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS B 145 GLN B 186 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7512 Z= 0.192 Angle : 0.784 12.551 10210 Z= 0.376 Chirality : 0.045 0.229 1200 Planarity : 0.006 0.056 1254 Dihedral : 8.149 55.881 1050 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.40 % Favored : 93.38 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -4.03 (0.22), residues: 922 helix: -2.47 (0.18), residues: 501 sheet: -1.12 (0.71), residues: 50 loop : -3.06 (0.28), residues: 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 172 average time/residue: 0.2054 time to fit residues: 47.0259 Evaluate side-chains 128 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0810 time to fit residues: 2.6970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7512 Z= 0.203 Angle : 0.720 9.695 10210 Z= 0.344 Chirality : 0.044 0.216 1200 Planarity : 0.005 0.046 1254 Dihedral : 7.754 59.214 1050 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.41 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -3.07 (0.24), residues: 922 helix: -1.53 (0.20), residues: 506 sheet: -0.71 (0.72), residues: 51 loop : -2.88 (0.29), residues: 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.2135 time to fit residues: 35.8404 Evaluate side-chains 118 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0695 time to fit residues: 2.4266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 68.7136 > 50: distance: 34 - 39: 29.680 distance: 39 - 40: 9.315 distance: 40 - 41: 38.402 distance: 40 - 43: 13.027 distance: 41 - 42: 43.435 distance: 41 - 44: 8.476 distance: 44 - 45: 35.275 distance: 45 - 46: 13.386 distance: 45 - 48: 31.227 distance: 46 - 47: 20.306 distance: 46 - 53: 35.702 distance: 48 - 49: 51.378 distance: 49 - 50: 20.171 distance: 50 - 51: 4.854 distance: 51 - 52: 12.413 distance: 53 - 54: 25.444 distance: 53 - 156: 15.199 distance: 54 - 55: 19.397 distance: 54 - 57: 25.698 distance: 55 - 56: 31.728 distance: 55 - 58: 22.664 distance: 56 - 153: 29.032 distance: 58 - 59: 22.043 distance: 59 - 60: 11.894 distance: 59 - 62: 15.747 distance: 60 - 61: 23.922 distance: 60 - 66: 22.070 distance: 62 - 63: 19.267 distance: 63 - 64: 33.356 distance: 63 - 65: 18.703 distance: 66 - 67: 24.965 distance: 67 - 68: 32.307 distance: 67 - 70: 17.014 distance: 68 - 69: 34.561 distance: 68 - 74: 38.183 distance: 70 - 71: 12.642 distance: 71 - 72: 28.214 distance: 71 - 73: 21.406 distance: 74 - 75: 27.508 distance: 75 - 76: 12.456 distance: 75 - 78: 11.911 distance: 76 - 77: 42.921 distance: 76 - 82: 16.973 distance: 78 - 79: 27.656 distance: 79 - 80: 25.707 distance: 79 - 81: 12.673 distance: 82 - 83: 25.871 distance: 82 - 204: 15.125 distance: 83 - 84: 19.283 distance: 83 - 86: 22.899 distance: 84 - 85: 12.923 distance: 84 - 90: 24.935 distance: 86 - 87: 23.866 distance: 87 - 88: 8.927 distance: 87 - 89: 11.558 distance: 90 - 91: 23.842 distance: 91 - 92: 10.973 distance: 91 - 94: 31.734 distance: 92 - 93: 21.057 distance: 92 - 96: 19.797 distance: 94 - 95: 7.686 distance: 96 - 97: 8.524 distance: 97 - 98: 26.557 distance: 97 - 100: 40.952 distance: 98 - 99: 21.687 distance: 98 - 103: 46.699 distance: 100 - 101: 27.196 distance: 100 - 102: 18.954 distance: 103 - 104: 29.954 distance: 104 - 105: 40.621 distance: 104 - 107: 64.152 distance: 105 - 106: 4.255 distance: 105 - 112: 35.119 distance: 107 - 108: 25.600 distance: 108 - 109: 16.020 distance: 109 - 110: 26.956 distance: 109 - 111: 40.359