Starting phenix.real_space_refine on Sat Oct 11 10:53:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy7_42794/10_2025/8uy7_42794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy7_42794/10_2025/8uy7_42794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uy7_42794/10_2025/8uy7_42794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy7_42794/10_2025/8uy7_42794.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy7_42794/10_2025/8uy7_42794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy7_42794/10_2025/8uy7_42794.cif" } resolution = 2.93 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 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= 0.009 sd= 0.114 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 Mg 6 5.21 5 S 76 5.16 5 C 8865 2.51 5 N 2358 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6912 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 6915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6915 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Time building chain proxies: 3.61, per 1000 atoms: 0.26 Number of scatterers: 14033 At special positions: 0 Unit cell: (97.11, 123.67, 130.31, 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 76 16.00 Mg 6 11.99 O 2728 8.00 N 2358 7.00 C 8865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.17 Conformation dependent library (CDL) restraints added in 667.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 10 sheets defined 56.1% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.509A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 4.186A pdb=" N TRP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 81 through 85 removed outlier: 4.126A pdb=" N GLN A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.554A pdb=" N THR A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 153 removed outlier: 3.645A pdb=" N VAL A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 279 through 312 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 313 through 326 removed outlier: 3.944A pdb=" N LEU A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Proline residue: A 330 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.102A pdb=" N MET A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.686A pdb=" N ASN A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.628A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.766A pdb=" N VAL A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.660A pdb=" N GLU A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 597' Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.740A pdb=" N GLN A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 629 Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 677 through 717 Processing helix chain 'A' and resid 726 through 742 Processing helix chain 'A' and resid 743 through 747 Processing helix chain 'A' and resid 762 through 773 removed outlier: 4.315A pdb=" N GLY A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 790 removed outlier: 3.853A pdb=" N PHE A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 798 through 817 removed outlier: 3.774A pdb=" N PHE A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 855 through 860 removed outlier: 4.364A pdb=" N TYR A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 4.242A pdb=" N TRP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.671A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 4.158A pdb=" N TRP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.054A pdb=" N GLN B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.995A pdb=" N LEU B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 153 removed outlier: 3.559A pdb=" N VAL B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.689A pdb=" N GLU B 235 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 279 through 312 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.925A pdb=" N LEU B 319 " --> pdb=" O TRP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 Proline residue: B 330 - end of helix No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 331 through 350 removed outlier: 3.983A pdb=" N MET B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.698A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.617A pdb=" N LEU B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.738A pdb=" N VAL B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 550 through 561 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.814A pdb=" N THR B 598 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 611 removed outlier: 3.852A pdb=" N GLN B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 629 Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'B' and resid 677 through 717 Processing helix chain 'B' and resid 726 through 742 Processing helix chain 'B' and resid 743 through 747 Processing helix chain 'B' and resid 762 through 790 removed outlier: 4.319A pdb=" N GLY B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Proline residue: B 774 - end of helix removed outlier: 3.849A pdb=" N PHE B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 798 through 817 removed outlier: 3.826A pdb=" N PHE B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 809 " --> pdb=" O GLY B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 855 through 860 removed outlier: 4.374A pdb=" N TYR B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 4.381A pdb=" N TRP B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.667A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.667A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.605A pdb=" N GLY A 655 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A 673 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 657 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 636 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 656 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 638 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL A 658 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 370 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 568 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR A 372 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N PHE A 614 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A 567 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 591 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 389 removed outlier: 3.923A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 515 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR A 540 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 513 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 542 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A 511 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA A 457 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS A 439 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 389 removed outlier: 3.923A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N CYS A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 537 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLN A 480 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY A 539 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ARG A 482 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 12.413A pdb=" N ILE A 541 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.691A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 245 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 206 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 204 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 251 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 202 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 253 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU B 200 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL B 255 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 198 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.691A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 245 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 206 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 204 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 251 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 202 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 253 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU B 200 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL B 255 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 198 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.645A pdb=" N GLY B 655 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 673 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 657 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 636 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE B 656 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE B 638 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL B 658 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B 370 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 568 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR B 372 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N PHE B 614 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 567 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B 591 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.916A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 515 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR B 540 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 513 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 542 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG B 511 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER B 453 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU B 442 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 455 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.916A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N CYS B 478 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 537 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN B 480 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY B 539 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ARG B 482 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 12.464A pdb=" N ILE B 541 " --> pdb=" O ARG B 482 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2256 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: 3.03 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2297 1.30 - 1.43: 3401 1.43 - 1.56: 8287 1.56 - 1.68: 0 1.68 - 1.81: 132 Bond restraints: 14117 Sorted by residual: bond pdb=" C ASN A 506 " pdb=" O ASN A 506 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.29e-02 6.01e+03 1.96e+01 bond pdb=" C ASN A 387 " pdb=" O ASN A 387 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.12e-02 7.97e+03 1.89e+01 bond pdb=" C HIS B 388 " pdb=" O HIS B 388 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.23e-02 6.61e+03 1.55e+01 bond pdb=" C HIS A 388 " pdb=" O HIS A 388 " ideal model delta sigma weight residual 1.235 1.190 0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA THR B 823 " pdb=" C THR B 823 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.24e-02 6.50e+03 1.36e+01 ... (remaining 14112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18533 1.79 - 3.57: 581 3.57 - 5.36: 89 5.36 - 7.15: 16 7.15 - 8.93: 7 Bond angle restraints: 19226 Sorted by residual: angle pdb=" N ARG A 825 " pdb=" CA ARG A 825 " pdb=" CB ARG A 825 " ideal model delta sigma weight residual 110.39 101.77 8.62 1.59e+00 3.96e-01 2.94e+01 angle pdb=" N LEU B 23 " pdb=" CA LEU B 23 " pdb=" C LEU B 23 " ideal model delta sigma weight residual 110.31 103.10 7.21 1.38e+00 5.25e-01 2.73e+01 angle pdb=" C ASN A 387 " pdb=" CA ASN A 387 " pdb=" CB ASN A 387 " ideal model delta sigma weight residual 110.14 102.16 7.98 1.60e+00 3.91e-01 2.49e+01 angle pdb=" C GLN B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta sigma weight residual 119.76 124.70 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA ASN A 506 " pdb=" CB ASN A 506 " pdb=" CG ASN A 506 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.37e+01 ... (remaining 19221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 7759 16.98 - 33.95: 587 33.95 - 50.93: 117 50.93 - 67.91: 16 67.91 - 84.89: 7 Dihedral angle restraints: 8486 sinusoidal: 3280 harmonic: 5206 Sorted by residual: dihedral pdb=" N ASN A 164 " pdb=" C ASN A 164 " pdb=" CA ASN A 164 " pdb=" CB ASN A 164 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C ASN A 387 " pdb=" N ASN A 387 " pdb=" CA ASN A 387 " pdb=" CB ASN A 387 " ideal model delta harmonic sigma weight residual -122.60 -111.49 -11.11 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C ASN A 164 " pdb=" N ASN A 164 " pdb=" CA ASN A 164 " pdb=" CB ASN A 164 " ideal model delta harmonic sigma weight residual -122.60 -132.94 10.34 0 2.50e+00 1.60e-01 1.71e+01 ... (remaining 8483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2064 0.083 - 0.167: 195 0.167 - 0.250: 12 0.250 - 0.334: 2 0.334 - 0.417: 1 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA ASN A 164 " pdb=" N ASN A 164 " pdb=" C ASN A 164 " pdb=" CB ASN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA PRO A 100 " pdb=" N PRO A 100 " pdb=" C PRO A 100 " pdb=" CB PRO A 100 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLN B 528 " pdb=" N GLN B 528 " pdb=" C GLN B 528 " pdb=" CB GLN B 528 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2271 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 528 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLN B 528 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN B 528 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 529 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 488 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 489 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 489 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 489 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 449 " 0.198 9.50e-02 1.11e+02 8.89e-02 4.91e+00 pdb=" NE ARG A 449 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 449 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 449 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 449 " 0.006 2.00e-02 2.50e+03 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 195 2.63 - 3.19: 12574 3.19 - 3.76: 22162 3.76 - 4.33: 30808 4.33 - 4.90: 51704 Nonbonded interactions: 117443 Sorted by model distance: nonbonded pdb=" OD1 ASN A 709 " pdb="MG MG A1001 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASN B 709 " pdb="MG MG B1001 " model vdw 2.069 2.170 nonbonded pdb=" OD1 ASP A 441 " pdb="MG MG A1003 " model vdw 2.108 2.170 nonbonded pdb=" OD1 ASP B 191 " pdb="MG MG B1002 " model vdw 2.196 2.170 nonbonded pdb=" OD1 ASP B 426 " pdb=" OG SER B 429 " model vdw 2.198 3.040 ... (remaining 117438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 164 or (resid 165 through 166 and (name N or nam \ e CA or name C or name O or name CB )) or resid 167 through 1003)) } 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: 3.900 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.980 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.005 0.057 14117 Z= 0.295 Angle : 0.738 8.934 19226 Z= 0.457 Chirality : 0.048 0.417 2274 Planarity : 0.006 0.089 2449 Dihedral : 12.806 84.887 5102 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 1.15 % Favored : 98.51 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1792 helix: 1.10 (0.18), residues: 884 sheet: -0.33 (0.33), residues: 194 loop : -0.65 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.017 0.001 TYR B 698 PHE 0.017 0.001 PHE B 364 TRP 0.009 0.001 TRP A 89 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00459 (14117) covalent geometry : angle 0.73765 (19226) hydrogen bonds : bond 0.15213 ( 747) hydrogen bonds : angle 6.63030 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 283 time to evaluate : 0.556 Fit side-chains REVERT: A 203 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7310 (tmt170) REVERT: A 247 VAL cc_start: 0.8975 (t) cc_final: 0.8752 (m) REVERT: A 487 ILE cc_start: 0.8965 (mm) cc_final: 0.8706 (mt) REVERT: A 632 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7382 (mt-10) REVERT: A 823 THR cc_start: 0.8978 (p) cc_final: 0.8573 (t) REVERT: A 895 TYR cc_start: 0.7048 (m-80) cc_final: 0.6729 (m-80) REVERT: B 49 PRO cc_start: 0.8820 (Cg_exo) cc_final: 0.8551 (Cg_endo) REVERT: B 62 GLU cc_start: 0.6610 (pt0) cc_final: 0.6239 (pp20) REVERT: B 290 MET cc_start: 0.8660 (mmm) cc_final: 0.8459 (tpt) REVERT: B 823 THR cc_start: 0.8976 (p) cc_final: 0.8742 (t) REVERT: B 895 TYR cc_start: 0.7133 (m-80) cc_final: 0.6799 (m-80) outliers start: 5 outliers final: 1 residues processed: 288 average time/residue: 0.6379 time to fit residues: 200.3413 Evaluate side-chains 176 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8452 > 50: distance: 5 - 13: 12.357 distance: 13 - 14: 13.385 distance: 14 - 15: 7.930 distance: 14 - 17: 12.351 distance: 15 - 16: 18.676 distance: 15 - 24: 19.059 distance: 17 - 18: 23.057 distance: 18 - 19: 14.073 distance: 19 - 20: 22.448 distance: 20 - 21: 39.925 distance: 21 - 22: 31.610 distance: 21 - 23: 31.954 distance: 24 - 25: 40.734 distance: 25 - 26: 43.970 distance: 25 - 28: 20.925 distance: 26 - 27: 31.424 distance: 26 - 32: 53.489 distance: 28 - 29: 8.209 distance: 29 - 30: 11.597 distance: 29 - 31: 11.097 distance: 32 - 33: 41.400 distance: 32 - 38: 29.696 distance: 33 - 34: 44.824 distance: 33 - 36: 18.494 distance: 34 - 35: 52.950 distance: 34 - 39: 18.067 distance: 36 - 37: 15.039 distance: 37 - 38: 7.915 distance: 39 - 40: 11.623 distance: 40 - 41: 21.911 distance: 40 - 43: 48.613 distance: 41 - 42: 18.049 distance: 41 - 47: 11.403 distance: 43 - 44: 31.074 distance: 44 - 45: 36.034 distance: 44 - 46: 35.965 distance: 47 - 48: 11.318 distance: 47 - 53: 19.576 distance: 48 - 49: 18.673 distance: 48 - 51: 22.904 distance: 49 - 50: 43.943 distance: 49 - 54: 35.548 distance: 51 - 52: 25.852 distance: 52 - 53: 15.164 distance: 54 - 55: 40.838 distance: 55 - 56: 43.008 distance: 56 - 57: 13.037 distance: 56 - 58: 36.373 distance: 58 - 59: 29.999 distance: 59 - 60: 16.316 distance: 59 - 62: 29.487 distance: 60 - 61: 13.350 distance: 60 - 63: 12.304 distance: 63 - 64: 4.782 distance: 64 - 65: 16.855 distance: 64 - 67: 20.906 distance: 65 - 66: 18.699 distance: 65 - 68: 10.993 distance: 68 - 69: 15.404 distance: 69 - 70: 9.995 distance: 69 - 72: 26.953 distance: 70 - 71: 24.217 distance: 70 - 73: 26.293 distance: 73 - 74: 27.600 distance: 74 - 75: 19.969 distance: 74 - 77: 31.459 distance: 75 - 76: 26.338 distance: 75 - 78: 9.121 distance: 154 - 162: 3.077