Starting phenix.real_space_refine on Sat Aug 23 11:02:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6j_41069/08_2025/8t6j_41069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6j_41069/08_2025/8t6j_41069.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2025/8t6j_41069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2025/8t6j_41069.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2025/8t6j_41069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2025/8t6j_41069.cif" } resolution = 3.5 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= 0.000 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. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 6, 'GLU:plan': 8, 'PHE:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 4, 'TRP:plan': 1} 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: {'ARG:plan': 6, 'GLU:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 4, 'TRP:plan': 1} 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: 2.75, per 1000 atoms: 0.24 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 - 3.00 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: 0.89 Conformation dependent library (CDL) restraints added in 509.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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... Secondary structure from input PDB file: 58 helices and 18 sheets defined 51.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.670A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.500A pdb=" N ALA B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.896A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.889A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.975A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 281 through 294 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 334 through 342 removed outlier: 4.378A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) 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 345 through 349 removed outlier: 3.807A pdb=" N ASN B 349 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.923A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) 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 433 through 443 removed outlier: 3.929A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) 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) removed outlier: 4.005A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.833A pdb=" N VAL B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.694A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 630 Processing helix chain 'B' and resid 631 through 637 removed outlier: 3.723A pdb=" N ALA B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 4.223A pdb=" N CYS B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) 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 689 through 715 removed outlier: 3.535A pdb=" N GLN B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 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 765 through 793 removed outlier: 3.594A pdb=" N ASN B 769 " --> pdb=" O PRO B 765 " (cutoff:3.500A) 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 797 through 816 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 818 through 827 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.742A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 101 through 117 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 153 through 163 removed outlier: 3.883A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.893A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.729A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 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 310 through 314 removed outlier: 3.558A pdb=" N VAL A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 4.388A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) 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 345 through 349 removed outlier: 3.790A pdb=" N ASN A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.930A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) 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 426 through 430 removed outlier: 4.072A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 3.895A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) 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) removed outlier: 3.987A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.859A pdb=" N VAL A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.697A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.662A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 4.241A pdb=" N CYS A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) 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 689 through 715 removed outlier: 3.523A pdb=" N GLN A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 761 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 765 through 793 removed outlier: 3.582A pdb=" N ASN A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) 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 797 through 816 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 818 through 827 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.262A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 213 through 216 removed outlier: 7.768A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.291A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (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=AA4, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AA5, 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=AA6, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA7, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AA9, 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=AB1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.258A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 213 through 216 removed outlier: 7.759A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) 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) Processing sheet with id=AB4, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) 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=AB5, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AB7, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB8, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AB9, 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) 534 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.15 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=" C19 YKU B 901 " pdb=" C21 YKU B 901 " ideal model delta sigma weight residual 1.429 1.527 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C19 YKU A 901 " pdb=" C21 YKU A 901 " ideal model delta sigma weight residual 1.429 1.526 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C13 YKU A 901 " pdb=" N12 YKU A 901 " ideal model delta sigma weight residual 1.359 1.454 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 YKU B 901 " pdb=" N12 YKU B 901 " ideal model delta sigma weight residual 1.359 1.453 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C04 YKU B 901 " pdb=" C07 YKU B 901 " ideal model delta sigma weight residual 1.465 1.528 -0.063 2.00e-02 2.50e+03 9.87e+00 ... (remaining 11913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 15964 2.00 - 4.00: 222 4.00 - 6.00: 19 6.00 - 7.99: 3 7.99 - 9.99: 2 Bond angle restraints: 16210 Sorted by residual: 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 angle pdb=" CA LEU B 295 " pdb=" CB LEU B 295 " pdb=" CG LEU B 295 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.15e+00 angle pdb=" CB ARG B 114 " pdb=" CG ARG B 114 " pdb=" CD ARG B 114 " ideal model delta sigma weight residual 111.30 104.76 6.54 2.30e+00 1.89e-01 8.09e+00 angle pdb=" CB MET A 474 " pdb=" CG MET A 474 " pdb=" SD MET A 474 " ideal model delta sigma weight residual 112.70 121.19 -8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" CB LYS A 51 " pdb=" CG LYS A 51 " pdb=" CD LYS A 51 " ideal model delta sigma weight residual 111.30 117.26 -5.96 2.30e+00 1.89e-01 6.71e+00 ... (remaining 16205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6401 17.97 - 35.94: 567 35.94 - 53.91: 105 53.91 - 71.88: 20 71.88 - 89.85: 3 Dihedral angle restraints: 7096 sinusoidal: 2638 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 7093 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: 11449 3.28 - 3.82: 18007 3.82 - 4.36: 19638 4.36 - 4.90: 36335 Nonbonded interactions: 86220 Sorted by model distance: nonbonded pdb=" OG SER B 152 " pdb=" OG SER B 176 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 176 " model vdw 2.221 3.040 nonbonded pdb=" O ARG B 435 " pdb=" NH1 ARG B 435 " model vdw 2.228 3.120 nonbonded pdb=" O ARG A 435 " pdb=" NH1 ARG A 435 " model vdw 2.229 3.120 nonbonded pdb=" O GLY A 253 " pdb=" OG SER A 256 " model vdw 2.274 3.040 ... (remaining 86215 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' 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 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 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: 3.130 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- 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 0.098 11934 Z= 0.169 Angle : 0.564 9.992 16242 Z= 0.290 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.036 2058 Dihedral : 13.807 89.854 4184 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 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: -0.00 (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 ARG 0.013 0.001 ARG B 114 TYR 0.010 0.001 TYR B 223 PHE 0.013 0.001 PHE B 544 TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00350 (11918) covalent geometry : angle 0.56267 (16210) SS BOND : bond 0.00179 ( 16) SS BOND : angle 1.03347 ( 32) hydrogen bonds : bond 0.14829 ( 527) hydrogen bonds : angle 5.56016 ( 1527) *********************** 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 to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.408 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: 0.0880 time to fit residues: 20.7615 Evaluate side-chains 124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 70.4482 > 50: distance: 2 - 19: 22.762 distance: 6 - 24: 18.123 distance: 11 - 30: 23.760 distance: 14 - 19: 20.828 distance: 15 - 38: 27.473 distance: 19 - 20: 8.508 distance: 20 - 21: 21.283 distance: 20 - 23: 27.591 distance: 21 - 22: 15.051 distance: 21 - 24: 14.718 distance: 22 - 42: 19.292 distance: 24 - 25: 10.745 distance: 25 - 26: 27.797 distance: 25 - 28: 35.926 distance: 26 - 27: 18.210 distance: 26 - 30: 12.458 distance: 27 - 50: 18.646 distance: 28 - 29: 5.418 distance: 30 - 31: 9.149 distance: 31 - 32: 15.137 distance: 31 - 34: 26.411 distance: 32 - 33: 24.674 distance: 32 - 38: 32.840 distance: 33 - 55: 45.487 distance: 34 - 35: 18.753 distance: 35 - 36: 43.354 distance: 35 - 37: 9.612 distance: 38 - 39: 3.768 distance: 39 - 40: 20.923 distance: 40 - 41: 25.264 distance: 40 - 42: 5.751 distance: 41 - 60: 48.181 distance: 42 - 43: 15.247 distance: 43 - 44: 4.034 distance: 43 - 46: 12.586 distance: 44 - 45: 44.858 distance: 44 - 50: 3.233 distance: 45 - 67: 7.408 distance: 46 - 47: 6.102 distance: 47 - 48: 7.501 distance: 50 - 51: 46.006 distance: 51 - 52: 27.319 distance: 51 - 54: 18.759 distance: 52 - 53: 8.653 distance: 52 - 55: 29.087 distance: 53 - 72: 30.572 distance: 55 - 56: 37.546 distance: 56 - 57: 20.054 distance: 56 - 59: 33.016 distance: 57 - 58: 12.230 distance: 57 - 60: 50.134 distance: 58 - 83: 28.399 distance: 60 - 61: 46.966 distance: 61 - 64: 43.139 distance: 62 - 63: 21.238 distance: 62 - 67: 31.942 distance: 63 - 90: 32.545 distance: 64 - 66: 18.487 distance: 67 - 68: 18.529 distance: 68 - 69: 18.542 distance: 68 - 71: 39.163 distance: 69 - 70: 14.708 distance: 69 - 72: 11.590 distance: 70 - 97: 22.386 distance: 72 - 73: 20.709 distance: 73 - 74: 8.128 distance: 73 - 76: 21.187 distance: 74 - 75: 10.219 distance: 74 - 83: 18.923 distance: 75 - 104: 22.749 distance: 76 - 77: 4.209 distance: 77 - 78: 25.278 distance: 77 - 79: 10.417 distance: 79 - 81: 34.523 distance: 81 - 82: 14.690