Starting phenix.real_space_refine on Sun Jul 21 15:06:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/07_2024/8sww_40823.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/07_2024/8sww_40823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/07_2024/8sww_40823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/07_2024/8sww_40823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/07_2024/8sww_40823.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sww_40823/07_2024/8sww_40823.cif" } resolution = 3.4 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= 0.002 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 102 5.16 5 C 9229 2.51 5 N 2565 2.21 5 O 2903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14799 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3478 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "C" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 927 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3490 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 829 Classifications: {'peptide': 105} Link IDs: {'TRANS': 104} Chain breaks: 2 Chain: "F" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3427 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 3 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.08, per 1000 atoms: 0.61 Number of scatterers: 14799 At special positions: 0 Unit cell: (134.03, 139.185, 119.596, 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 102 16.00 O 2903 8.00 N 2565 7.00 C 9229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.12 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.08 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.01 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.02 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 152 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 637 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 448 " " NAG E 603 " - " ASN E 332 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 88 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 152 " " NAG F 603 " - " ASN F 295 " " NAG F 604 " - " ASN F 301 " " NAG F 605 " - " ASN F 339 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 241 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 234 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " " NAG O 1 " - " ASN F 332 " Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 2.2 seconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 27 sheets defined 26.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.590A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.963A pdb=" N ARG A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.168A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.313A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.768A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.722A pdb=" N THR B 536 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.524A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.220A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 535 Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 570 through 596 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 656 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 334 through 350 removed outlier: 4.916A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 474 through 481 removed outlier: 3.532A pdb=" N TRP E 479 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.243A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.740A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 544 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 638 through 654 Processing helix chain 'F' and resid 98 through 116 removed outlier: 3.593A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.834A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'L' and resid 61 through 64 removed outlier: 3.976A pdb=" N UNK L 64 " --> pdb=" O UNK L 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 61 through 64' Processing helix chain 'L' and resid 83 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 495 removed outlier: 5.099A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.349A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.455A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.668A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.245A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AB4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.514A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 298 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 333 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AB6, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.456A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.448A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 161 through 169 removed outlier: 4.518A pdb=" N GLU F 190 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.132A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 4.359A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 321 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AC7, first strand: chain 'H' and resid 36 through 41 removed outlier: 5.529A pdb=" N UNK H 36 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N UNK H 52 " --> pdb=" O UNK H 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N UNK H 38 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 57 current: chain 'H' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'L' and resid 32 through 39 removed outlier: 7.360A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 57 through 59 current: chain 'L' and resid 105 through 106 444 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3892 1.33 - 1.47: 4556 1.47 - 1.61: 6457 1.61 - 1.75: 22 1.75 - 1.89: 127 Bond restraints: 15054 Sorted by residual: bond pdb=" CB LEU D 568 " pdb=" CG LEU D 568 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.59e+01 bond pdb=" CB LEU B 568 " pdb=" CG LEU B 568 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.25e+01 bond pdb=" CB ASN F 289 " pdb=" CG ASN F 289 " ideal model delta sigma weight residual 1.516 1.362 0.154 2.50e-02 1.60e+03 3.78e+01 ... (remaining 15049 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.71: 549 106.71 - 113.61: 8193 113.61 - 120.51: 6237 120.51 - 127.41: 5301 127.41 - 134.31: 192 Bond angle restraints: 20472 Sorted by residual: angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.60 -8.04 1.01e+00 9.80e-01 6.34e+01 angle pdb=" N TRP D 628 " pdb=" CA TRP D 628 " pdb=" C TRP D 628 " ideal model delta sigma weight residual 110.50 99.80 10.70 1.41e+00 5.03e-01 5.75e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 124.88 -5.22 7.30e-01 1.88e+00 5.12e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 126.62 -7.06 1.01e+00 9.80e-01 4.88e+01 angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 111.81 117.68 -5.87 8.60e-01 1.35e+00 4.66e+01 ... (remaining 20467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 9397 21.88 - 43.77: 161 43.77 - 65.65: 47 65.65 - 87.54: 27 87.54 - 109.42: 9 Dihedral angle restraints: 9641 sinusoidal: 4192 harmonic: 5449 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -175.12 89.12 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual 93.00 174.10 -81.10 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -130.47 44.47 1 1.00e+01 1.00e-02 2.75e+01 ... (remaining 9638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1753 0.102 - 0.204: 497 0.204 - 0.306: 138 0.306 - 0.408: 75 0.408 - 0.510: 27 Chirality restraints: 2490 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 ... (remaining 2487 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 241 " 0.099 2.00e-02 2.50e+03 1.06e-01 1.40e+02 pdb=" CG ASN F 241 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN F 241 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN F 241 " -0.166 2.00e-02 2.50e+03 pdb=" C1 NAG F 607 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " 0.077 2.00e-02 2.50e+03 8.02e-02 8.05e+01 pdb=" CG ASN E 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " -0.125 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 339 " 0.070 2.00e-02 2.50e+03 7.22e-02 6.52e+01 pdb=" CG ASN F 339 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN F 339 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 339 " -0.111 2.00e-02 2.50e+03 pdb=" C1 NAG F 605 " 0.088 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2728 2.76 - 3.30: 13386 3.30 - 3.83: 23299 3.83 - 4.37: 28990 4.37 - 4.90: 46438 Nonbonded interactions: 114841 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.231 2.440 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.386 2.496 nonbonded pdb=" N GLU E 482 " pdb=" O GLU E 482 " model vdw 2.397 2.496 nonbonded pdb=" O4 BMA N 3 " pdb=" O6 BMA N 3 " model vdw 2.403 2.440 nonbonded pdb=" OD2 ASP C 632 " pdb=" NZ LYS E 46 " model vdw 2.422 2.520 ... (remaining 114836 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 'A' and (resid 36 through 58 or resid 66 through 411 or resid 413 through \ 501 or resid 602 through 607)) selection = (chain 'E' and (resid 36 through 154 or resid 159 through 176 or resid 189 throu \ gh 501 or resid 601 through 606)) selection = (chain 'F' and (resid 36 through 154 or resid 159 through 176 or resid 189 throu \ gh 398 or resid 413 through 501 or resid 604 through 609)) } ncs_group { reference = (chain 'B' and (resid 522 through 547 or resid 569 through 608 or resid 620 thro \ ugh 657)) selection = (chain 'C' and (resid 522 through 608 or resid 620 through 657)) selection = (chain 'D' and (resid 522 through 547 or resid 569 through 657)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 4 through 114) } 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: 7.380 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.830 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.280 ------------------------------------------------------------------------------- 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 : 0.021 0.154 15054 Z= 1.334 Angle : 1.685 11.834 20472 Z= 1.096 Chirality : 0.124 0.510 2490 Planarity : 0.009 0.050 2577 Dihedral : 10.733 109.419 5996 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.60 (0.20), residues: 1619 helix: -0.07 (0.26), residues: 369 sheet: 1.26 (0.23), residues: 417 loop : 0.29 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP A 69 HIS 0.015 0.002 HIS A 374 PHE 0.032 0.007 PHE E 376 TYR 0.041 0.007 TYR F 191 ARG 0.009 0.001 ARG C 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8535 (m-80) cc_final: 0.8331 (m-80) REVERT: A 347 LYS cc_start: 0.8462 (tttt) cc_final: 0.8256 (ttmm) REVERT: A 434 MET cc_start: 0.9062 (ttp) cc_final: 0.8809 (ttm) REVERT: E 128 THR cc_start: 0.9024 (m) cc_final: 0.8816 (p) REVERT: E 138 ILE cc_start: 0.6305 (mm) cc_final: 0.6094 (mm) REVERT: E 274 SER cc_start: 0.8326 (t) cc_final: 0.8122 (p) REVERT: E 351 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7484 (ttmm) REVERT: E 500 ARG cc_start: 0.6413 (mmt180) cc_final: 0.5708 (mtt180) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2855 time to fit residues: 194.3470 Evaluate side-chains 283 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.642 > 50: distance: 34 - 39: 13.344 distance: 39 - 40: 27.187 distance: 40 - 41: 35.095 distance: 40 - 43: 42.360 distance: 41 - 42: 54.356 distance: 41 - 48: 17.695 distance: 43 - 44: 32.293 distance: 44 - 45: 9.569 distance: 45 - 46: 15.090 distance: 46 - 47: 29.577 distance: 48 - 49: 36.456 distance: 48 - 54: 30.470 distance: 49 - 50: 27.451 distance: 49 - 52: 8.926 distance: 50 - 51: 38.652 distance: 50 - 55: 37.440 distance: 52 - 53: 54.405 distance: 53 - 54: 16.920 distance: 55 - 56: 25.350 distance: 56 - 57: 14.529 distance: 56 - 59: 14.827 distance: 57 - 62: 31.078 distance: 59 - 60: 18.067 distance: 59 - 61: 5.863 distance: 62 - 63: 15.932 distance: 63 - 64: 10.548 distance: 63 - 66: 24.151 distance: 64 - 65: 17.166 distance: 64 - 69: 31.347 distance: 66 - 67: 34.096 distance: 66 - 68: 40.386 distance: 69 - 70: 24.455 distance: 70 - 71: 22.571 distance: 70 - 73: 39.165 distance: 71 - 72: 42.735 distance: 71 - 75: 28.805 distance: 73 - 74: 36.222 distance: 75 - 76: 22.759 distance: 76 - 77: 21.573 distance: 76 - 79: 26.743 distance: 77 - 78: 17.362 distance: 77 - 82: 34.592 distance: 79 - 80: 39.430 distance: 79 - 81: 59.032 distance: 82 - 83: 26.015 distance: 83 - 84: 13.080 distance: 83 - 86: 37.535 distance: 84 - 85: 31.784 distance: 84 - 91: 28.599 distance: 86 - 87: 39.004 distance: 87 - 88: 7.284 distance: 88 - 89: 21.985 distance: 88 - 90: 38.843 distance: 91 - 92: 26.271 distance: 92 - 93: 16.672 distance: 92 - 95: 8.376 distance: 93 - 94: 29.130 distance: 93 - 99: 9.429 distance: 95 - 96: 36.762 distance: 96 - 97: 31.310 distance: 96 - 98: 32.525 distance: 99 - 100: 7.159 distance: 100 - 101: 16.387 distance: 100 - 103: 34.223 distance: 101 - 102: 32.352 distance: 101 - 107: 33.662 distance: 103 - 104: 35.782 distance: 104 - 105: 39.687 distance: 104 - 106: 12.905 distance: 107 - 108: 36.303 distance: 108 - 109: 17.854 distance: 108 - 111: 16.656 distance: 109 - 110: 23.702 distance: 109 - 115: 30.021 distance: 111 - 112: 51.429 distance: 112 - 114: 36.972