Starting phenix.real_space_refine on Thu May 9 01:14:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6j_41069/05_2024/8t6j_41069_updated.pdb" } resolution = 3.5 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= 1.000 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 112 5.16 5 C 7473 2.51 5 N 1940 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 498": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5803 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5793 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 156 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.59, per 1000 atoms: 0.57 Number of scatterers: 11652 At special positions: 0 Unit cell: (123.555, 82.6537, 188.314, 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 112 16.00 O 2127 8.00 N 1940 7.00 C 7473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " 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: 5.52 Conformation dependent library (CDL) restraints added in 2.5 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 20 sheets defined 45.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 67 through 81 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.664A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.578A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.588A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 238 removed outlier: 3.975A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.707A pdb=" N SER B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.666A pdb=" N ARG B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.019A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 397 through 418 removed outlier: 3.940A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.875A pdb=" N LEU B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 578 through 603 Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 615 through 636 removed outlier: 3.757A pdb=" N CYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 672 removed outlier: 4.262A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.272A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 714 Processing helix chain 'B' and resid 738 through 760 Proline residue: B 743 - end of helix removed outlier: 4.097A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 750 " --> pdb=" O TYR B 746 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 792 removed outlier: 5.648A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 798 through 815 removed outlier: 3.931A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 826 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.685A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.585A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.588A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 238 removed outlier: 4.009A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.729A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 3.655A pdb=" N ARG A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.056A pdb=" N ASP A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.935A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 434 through 442 removed outlier: 3.856A pdb=" N LEU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 578 through 603 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 636 removed outlier: 3.771A pdb=" N CYS A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N CYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 672 removed outlier: 4.296A pdb=" N TYR A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 4.298A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 714 Processing helix chain 'A' and resid 738 through 760 Proline residue: A 743 - end of helix removed outlier: 4.044A pdb=" N LEU A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 750 " --> pdb=" O TYR A 746 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 792 removed outlier: 5.647A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 798 through 815 removed outlier: 3.927A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 Processing sheet with id= A, first strand: chain 'B' and resid 28 through 31 Processing sheet with id= B, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.496A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N CYS B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU B 302 " --> pdb=" O CYS B 276 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.812A pdb=" N THR B 326 " --> pdb=" O MET B 469 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 468 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 445 through 447 Processing sheet with id= F, first strand: chain 'B' and resid 520 through 522 Processing sheet with id= G, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= H, first strand: chain 'B' and resid 556 through 558 Processing sheet with id= I, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.609A pdb=" N ASP B 722 " --> pdb=" O TYR B 730 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 471 through 475 removed outlier: 3.570A pdb=" N LYS B 472 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 480 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 28 through 31 Processing sheet with id= L, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= M, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.581A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N CYS A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU A 302 " --> pdb=" O CYS A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 468 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= P, first strand: chain 'A' and resid 520 through 522 Processing sheet with id= Q, first strand: chain 'A' and resid 541 through 543 Processing sheet with id= R, first strand: chain 'A' and resid 556 through 558 Processing sheet with id= S, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.606A pdb=" N ASP A 722 " --> pdb=" O TYR A 730 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 471 through 475 removed outlier: 3.555A pdb=" N LYS A 472 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 480 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1341 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: 3.89 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1887 1.27 - 1.41: 3001 1.41 - 1.55: 6857 1.55 - 1.68: 11 1.68 - 1.82: 162 Bond restraints: 11918 Sorted by residual: bond pdb=" C07 YKU A 901 " pdb=" C11 YKU A 901 " ideal model delta sigma weight residual 1.366 1.393 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C07 YKU B 901 " pdb=" C11 YKU B 901 " ideal model delta sigma weight residual 1.366 1.392 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" N08 YKU A 901 " pdb=" N09 YKU A 901 " ideal model delta sigma weight residual 1.387 1.365 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" N08 YKU B 901 " pdb=" N09 YKU B 901 " ideal model delta sigma weight residual 1.387 1.366 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C VAL B 789 " pdb=" N PRO B 790 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.73e-01 ... (remaining 11913 not shown) Histogram of bond angle deviations from ideal: 98.74 - 114.85: 7432 114.85 - 130.96: 8725 130.96 - 147.07: 51 147.07 - 163.18: 0 163.18 - 179.29: 2 Bond angle restraints: 16210 Sorted by residual: angle pdb=" C10 YKU A 901 " pdb=" N09 YKU A 901 " pdb=" C23 YKU A 901 " ideal model delta sigma weight residual 141.24 125.30 15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C10 YKU B 901 " pdb=" N09 YKU B 901 " pdb=" C23 YKU B 901 " ideal model delta sigma weight residual 141.24 125.39 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C23 YKU A 901 " pdb=" N09 YKU A 901 " pdb=" N08 YKU A 901 " ideal model delta sigma weight residual 110.12 124.17 -14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C23 YKU B 901 " pdb=" N09 YKU B 901 " pdb=" N08 YKU B 901 " ideal model delta sigma weight residual 110.12 124.11 -13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" CB LYS B 51 " pdb=" CG LYS B 51 " pdb=" CD LYS B 51 " ideal model delta sigma weight residual 111.30 117.90 -6.60 2.30e+00 1.89e-01 8.23e+00 ... (remaining 16205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6401 17.97 - 35.94: 559 35.94 - 53.91: 98 53.91 - 71.88: 19 71.88 - 89.85: 5 Dihedral angle restraints: 7082 sinusoidal: 2624 harmonic: 4458 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 135.61 -42.61 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual -86.00 -44.07 -41.93 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual 93.00 134.68 -41.68 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 7079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1000 0.027 - 0.054: 531 0.054 - 0.082: 203 0.082 - 0.109: 84 0.109 - 0.136: 34 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA ILE B 568 " pdb=" N ILE B 568 " pdb=" C ILE B 568 " pdb=" CB ILE B 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 568 " pdb=" N ILE A 568 " pdb=" C ILE A 568 " pdb=" CB ILE A 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL B 217 " pdb=" N VAL B 217 " pdb=" C VAL B 217 " pdb=" CB VAL B 217 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1849 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 789 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 790 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 790 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 790 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 789 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO B 790 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 790 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 790 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 764 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 765 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 791 2.74 - 3.28: 11497 3.28 - 3.82: 18062 3.82 - 4.36: 19783 4.36 - 4.90: 36367 Nonbonded interactions: 86500 Sorted by model distance: nonbonded pdb=" OG SER B 152 " pdb=" OG SER B 176 " model vdw 2.196 2.440 nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 176 " model vdw 2.221 2.440 nonbonded pdb=" O ARG B 435 " pdb=" NH1 ARG B 435 " model vdw 2.228 2.520 nonbonded pdb=" O ARG A 435 " pdb=" NH1 ARG A 435 " model vdw 2.229 2.520 nonbonded pdb=" O GLY A 253 " pdb=" OG SER A 256 " model vdw 2.274 2.440 ... (remaining 86495 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 26 through 515 or (resid 516 through 517 and (name N or na \ me CA or name C or name O or name CB )) or resid 518 through 827 or resid 901)) selection = (chain 'B' and (resid 26 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 552 or (resid 553 and (name N o \ r name CA or name C or name O or name CB )) or resid 554 through 559 or (resid 5 \ 60 through 561 and (name N or name CA or name C or name O or name CB )) or resid \ 562 through 827 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 9.800 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.930 Find NCS groups from input model: 0.670 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: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.003 0.029 11918 Z= 0.171 Angle : 0.603 15.941 16210 Z= 0.298 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.036 2058 Dihedral : 13.747 89.854 4170 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.00 (0.23), residues: 1522 helix: 1.52 (0.21), residues: 648 sheet: -1.22 (0.42), residues: 172 loop : -1.14 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS B 30 PHE 0.013 0.001 PHE B 544 TYR 0.010 0.001 TYR B 223 ARG 0.013 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: B 657 MET cc_start: 0.6699 (ptm) cc_final: 0.6420 (ptt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2143 time to fit residues: 49.6028 Evaluate side-chains 124 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 11918 Z= 0.591 Angle : 0.782 7.062 16210 Z= 0.409 Chirality : 0.050 0.152 1852 Planarity : 0.006 0.074 2058 Dihedral : 5.851 89.583 1648 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 1.90 % Allowed : 11.89 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.73 (0.22), residues: 1522 helix: 0.82 (0.21), residues: 660 sheet: -1.42 (0.40), residues: 178 loop : -1.51 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 487 HIS 0.006 0.002 HIS B 44 PHE 0.022 0.002 PHE A 712 TYR 0.022 0.002 TYR B 340 ARG 0.011 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 145 average time/residue: 0.2619 time to fit residues: 54.8171 Evaluate side-chains 135 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 60.8673 > 50: distance: 38 - 42: 9.500 distance: 42 - 43: 7.063 distance: 43 - 44: 5.531 distance: 43 - 46: 6.949 distance: 44 - 45: 12.061 distance: 44 - 50: 7.203 distance: 46 - 47: 7.888 distance: 47 - 48: 8.294 distance: 47 - 49: 6.427 distance: 50 - 51: 6.677 distance: 51 - 52: 4.796 distance: 51 - 54: 12.220 distance: 52 - 53: 4.962 distance: 52 - 55: 7.293 distance: 55 - 56: 9.755 distance: 56 - 57: 6.276 distance: 56 - 59: 10.484 distance: 57 - 58: 7.629 distance: 57 - 63: 6.903 distance: 59 - 60: 9.078 distance: 61 - 62: 11.859 distance: 63 - 64: 13.973 distance: 64 - 65: 15.507 distance: 64 - 67: 23.603 distance: 65 - 66: 23.235 distance: 65 - 72: 6.176 distance: 67 - 68: 10.599 distance: 69 - 70: 11.951 distance: 70 - 71: 28.843 distance: 72 - 73: 12.890 distance: 72 - 78: 18.884 distance: 73 - 74: 8.515 distance: 73 - 76: 8.713 distance: 74 - 75: 23.306 distance: 74 - 79: 6.769 distance: 76 - 77: 17.908 distance: 77 - 78: 20.371 distance: 79 - 80: 27.841 distance: 80 - 81: 16.146 distance: 80 - 83: 39.251 distance: 81 - 82: 12.716 distance: 81 - 87: 7.983 distance: 83 - 84: 23.140 distance: 83 - 85: 11.870 distance: 84 - 86: 32.648 distance: 87 - 88: 5.147 distance: 88 - 89: 26.706 distance: 88 - 91: 8.194 distance: 89 - 90: 3.767 distance: 89 - 95: 30.964 distance: 91 - 92: 19.720 distance: 92 - 93: 7.701 distance: 92 - 94: 3.576 distance: 95 - 96: 5.377 distance: 96 - 97: 11.921 distance: 97 - 98: 11.773 distance: 97 - 99: 25.361 distance: 99 - 100: 9.383 distance: 100 - 101: 5.710 distance: 101 - 102: 8.932 distance: 101 - 110: 6.936 distance: 103 - 104: 7.466 distance: 104 - 105: 11.909 distance: 105 - 106: 9.106 distance: 106 - 107: 7.805 distance: 107 - 108: 6.844 distance: 107 - 109: 6.583 distance: 110 - 111: 5.622 distance: 111 - 112: 4.097 distance: 111 - 114: 6.052 distance: 112 - 113: 8.699 distance: 112 - 119: 6.849 distance: 113 - 137: 15.502 distance: 114 - 115: 4.212 distance: 115 - 116: 8.882 distance: 116 - 117: 10.554 distance: 117 - 118: 6.037