Starting phenix.real_space_refine on Sat Jul 4 21:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wi1_21682/07_2026/6wi1_21682.cif" } resolution = 3.62 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= 0.032 sd= 0.873 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 130 5.16 5 C 14940 2.51 5 N 3856 2.21 5 O 4440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23366 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 5910 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 770} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 19, 'HIS:plan': 3, 'GLU:plan': 17, 'GLN:plan1': 8, 'ASN:plan1': 9, 'ASP:plan': 7, 'PHE:plan': 6, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 331 Chain: "B" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5661 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 18, 'HIS:plan': 6, 'PHE:plan': 8, 'ARG:plan': 12, 'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "C" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 5910 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 770} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 19, 'HIS:plan': 3, 'GLU:plan': 17, 'GLN:plan1': 8, 'ASN:plan1': 9, 'ASP:plan': 7, 'PHE:plan': 6, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 331 Chain: "D" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5661 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 18, 'HIS:plan': 6, 'PHE:plan': 8, 'ARG:plan': 12, 'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.85, per 1000 atoms: 0.25 Number of scatterers: 23366 At special positions: 0 Unit cell: (135.63, 149.33, 186.32, 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 130 16.00 O 4440 8.00 N 3856 7.00 C 14940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS B 795 " distance=2.00 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.05 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 719 " - pdb=" SG CYS D 795 " distance=2.09 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.05 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.05 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 901 " - " ASN A 224 " " NAG A 902 " - " ASN A 297 " " NAG B 903 " - " ASN B 491 " " NAG B 904 " - " ASN B 341 " " NAG C 901 " - " ASN C 224 " " NAG C 902 " - " ASN C 297 " " NAG D 903 " - " ASN D 491 " " NAG D 904 " - " ASN D 341 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN B 348 " " NAG G 1 " - " ASN D 688 " " NAG H 1 " - " ASN D 348 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 979.1 milliseconds 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 34 sheets defined 43.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.275A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.551A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.811A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.570A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.920A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 4.149A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.242A pdb=" N VAL A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 647 through 679 removed outlier: 4.044A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.069A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 862 removed outlier: 4.449A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.723A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.948A pdb=" N ASP B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS B 61 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 62 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 3.632A pdb=" N LYS B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.603A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.593A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.183A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.928A pdb=" N ILE B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.243A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.687A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.766A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.823A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 654 removed outlier: 4.016A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 714 through 724 removed outlier: 3.572A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.116A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.481A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 795 removed outlier: 3.585A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 3.857A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.274A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.552A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.811A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.570A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.921A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 4.149A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.242A pdb=" N VAL C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 647 through 679 removed outlier: 4.046A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C 677 " --> pdb=" O ALA C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 734 through 744 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.070A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 862 removed outlier: 4.451A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.723A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.949A pdb=" N ASP D 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS D 60 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 61 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 62 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.632A pdb=" N LYS D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.603A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.593A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 288 through 312 removed outlier: 4.183A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 removed outlier: 3.928A pdb=" N ILE D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 4.243A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.687A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.767A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 578 Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.823A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 654 removed outlier: 4.016A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 690 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 714 through 724 removed outlier: 3.572A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.117A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.481A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 795 removed outlier: 3.585A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 844 removed outlier: 3.858A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 removed outlier: 7.931A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 216 removed outlier: 7.505A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 269 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 242 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 3.712A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 434 removed outlier: 3.563A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 456 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU A 499 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR A 458 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 Processing sheet with id=AA7, first strand: chain 'A' and resid 549 through 550 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 removed outlier: 6.612A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 561 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 73 removed outlier: 7.768A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 204 removed outlier: 6.281A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 170 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.621A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 728 through 732 removed outlier: 3.543A pdb=" N LEU B 748 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 728 through 732 removed outlier: 5.017A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 61 removed outlier: 7.931A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 211 through 216 removed outlier: 7.505A pdb=" N ILE C 163 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 215 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 165 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 269 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 290 through 292 removed outlier: 3.711A pdb=" N GLY C 386 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.563A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 456 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU C 499 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR C 458 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 508 through 510 Processing sheet with id=AC6, first strand: chain 'C' and resid 549 through 550 Processing sheet with id=AC7, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC8, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.613A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 561 " --> pdb=" O THR C 770 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 73 removed outlier: 7.767A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 201 through 204 removed outlier: 6.281A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 170 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD3, first strand: chain 'D' and resid 408 through 409 Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.622A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD6, first strand: chain 'D' and resid 728 through 732 removed outlier: 3.544A pdb=" N LEU D 748 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 728 through 732 removed outlier: 5.016A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1074 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7574 1.34 - 1.47: 5765 1.47 - 1.59: 10295 1.59 - 1.71: 0 1.71 - 1.83: 216 Bond restraints: 23850 Sorted by residual: bond pdb=" C ILE A 401 " pdb=" N TRP A 402 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.86e-02 2.89e+03 9.07e+00 bond pdb=" C ILE C 401 " pdb=" N TRP C 402 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.86e-02 2.89e+03 8.93e+00 bond pdb=" CB TRP D 166 " pdb=" CG TRP D 166 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.43e+00 bond pdb=" CB TRP B 166 " pdb=" CG TRP B 166 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.34e+00 bond pdb=" CA PRO D 674 " pdb=" CB PRO D 674 " ideal model delta sigma weight residual 1.532 1.517 0.015 7.10e-03 1.98e+04 4.19e+00 ... (remaining 23845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 32040 2.65 - 5.31: 484 5.31 - 7.96: 46 7.96 - 10.62: 8 10.62 - 13.27: 4 Bond angle restraints: 32582 Sorted by residual: angle pdb=" C ILE D 85 " pdb=" N CYS D 86 " pdb=" CA CYS D 86 " ideal model delta sigma weight residual 121.14 111.58 9.56 1.75e+00 3.27e-01 2.98e+01 angle pdb=" C ILE B 85 " pdb=" N CYS B 86 " pdb=" CA CYS B 86 " ideal model delta sigma weight residual 121.14 111.58 9.56 1.75e+00 3.27e-01 2.98e+01 angle pdb=" CA CYS C 765 " pdb=" CB CYS C 765 " pdb=" SG CYS C 765 " ideal model delta sigma weight residual 114.40 126.66 -12.26 2.30e+00 1.89e-01 2.84e+01 angle pdb=" CA CYS A 765 " pdb=" CB CYS A 765 " pdb=" SG CYS A 765 " ideal model delta sigma weight residual 114.40 126.64 -12.24 2.30e+00 1.89e-01 2.83e+01 angle pdb=" C PRO A 468 " pdb=" N ARG A 469 " pdb=" CA ARG A 469 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 ... (remaining 32577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 12669 17.46 - 34.92: 1075 34.92 - 52.38: 166 52.38 - 69.83: 38 69.83 - 87.29: 18 Dihedral angle restraints: 13966 sinusoidal: 4768 harmonic: 9198 Sorted by residual: dihedral pdb=" CA LYS A 764 " pdb=" C LYS A 764 " pdb=" N CYS A 765 " pdb=" CA CYS A 765 " ideal model delta harmonic sigma weight residual 180.00 121.51 58.49 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA LYS C 764 " pdb=" C LYS C 764 " pdb=" N CYS C 765 " pdb=" CA CYS C 765 " ideal model delta harmonic sigma weight residual 180.00 121.56 58.44 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -7.29 -78.71 1 1.00e+01 1.00e-02 7.72e+01 ... (remaining 13963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.743: 3926 0.743 - 1.486: 0 1.486 - 2.229: 0 2.229 - 2.972: 0 2.972 - 3.715: 2 Chirality restraints: 3928 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 1.31 -3.71 2.00e-02 2.50e+03 3.45e+04 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 1.31 -3.71 2.00e-02 2.50e+03 3.44e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.88e+01 ... (remaining 3925 not shown) Planarity restraints: 4152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 813 " 0.023 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP C 813 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 813 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 813 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 813 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 813 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 813 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 813 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 813 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 813 " -0.022 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" CG TRP A 813 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 813 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 813 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 813 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 813 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 813 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 568 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " -0.033 5.00e-02 4.00e+02 ... (remaining 4149 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 831 2.68 - 3.24: 25441 3.24 - 3.79: 35411 3.79 - 4.35: 43273 4.35 - 4.90: 70471 Nonbonded interactions: 175427 Sorted by model distance: nonbonded pdb=" O ASP A 324 " pdb=" NE1 TRP A 336 " model vdw 2.127 3.120 nonbonded pdb=" O ASP C 324 " pdb=" NE1 TRP C 336 " model vdw 2.127 3.120 nonbonded pdb=" OD1 ASP D 77 " pdb=" N SER D 80 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASP B 77 " pdb=" N SER B 80 " model vdw 2.153 3.120 nonbonded pdb=" OD1 ASP D 101 " pdb=" N ASP D 102 " model vdw 2.188 3.120 ... (remaining 175422 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.730 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.007 0.065 23884 Z= 0.319 Angle : 0.995 57.599 32666 Z= 0.503 Chirality : 0.097 3.715 3928 Planarity : 0.005 0.061 4140 Dihedral : 13.822 87.292 7972 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.47 % Favored : 85.09 % Rotamer: Outliers : 0.70 % Allowed : 8.72 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -4.55 (0.12), residues: 3158 helix: -1.66 (0.12), residues: 1276 sheet: -4.13 (0.21), residues: 372 loop : -4.04 (0.12), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 693 TYR 0.019 0.002 TYR B 507 PHE 0.019 0.002 PHE C 774 TRP 0.044 0.002 TRP C 813 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.32 (23850) covalent geometry : angle 0.84480 / 0.47 (32582) SS BOND : bond 0.01797 / 1.35 ( 18) SS BOND : angle 2.50791 / 1.82 ( 36) hydrogen bonds : bond 0.16872 / 11.54 ( 1060) hydrogen bonds : angle 7.32779 / 5.20 ( 3102) link_BETA1-4 : bond 0.06393 / 3.20 ( 4) link_BETA1-4 : angle 26.45577 / 14.56 ( 12) link_NAG-ASN : bond 0.00480 / 0.33 ( 12) link_NAG-ASN : angle 3.63345 / 2.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8822 (mmm) cc_final: 0.8620 (mmm) REVERT: A 261 MET cc_start: 0.8444 (mmm) cc_final: 0.8207 (mmm) REVERT: A 287 ILE cc_start: 0.8699 (pt) cc_final: 0.8485 (mm) REVERT: A 375 MET cc_start: 0.8708 (mpp) cc_final: 0.8136 (mpp) REVERT: A 377 LEU cc_start: 0.8989 (tp) cc_final: 0.8760 (tp) REVERT: A 702 TYR cc_start: 0.8513 (m-80) cc_final: 0.8295 (m-80) REVERT: A 758 GLU cc_start: 0.8830 (tp30) cc_final: 0.8458 (tm-30) REVERT: A 783 MET cc_start: 0.8403 (mtm) cc_final: 0.8130 (mtp) REVERT: A 806 MET cc_start: 0.9258 (mmm) cc_final: 0.8887 (mmt) REVERT: B 89 MET cc_start: 0.9099 (ptp) cc_final: 0.8591 (ppp) REVERT: B 354 ASP cc_start: 0.9463 (m-30) cc_final: 0.9191 (m-30) REVERT: B 430 MET cc_start: 0.8400 (tmm) cc_final: 0.8055 (ttm) REVERT: B 789 MET cc_start: 0.8776 (mmm) cc_final: 0.8516 (mmt) REVERT: C 230 MET cc_start: 0.8825 (mmm) cc_final: 0.8591 (mmm) REVERT: C 261 MET cc_start: 0.8437 (mmm) cc_final: 0.8177 (mmm) REVERT: C 375 MET cc_start: 0.8619 (mpp) cc_final: 0.8289 (mpp) REVERT: C 758 GLU cc_start: 0.8902 (tp30) cc_final: 0.8514 (tm-30) REVERT: C 783 MET cc_start: 0.8521 (mtm) cc_final: 0.8294 (mtp) REVERT: C 806 MET cc_start: 0.9220 (mmm) cc_final: 0.8844 (mmt) REVERT: D 89 MET cc_start: 0.8973 (ptp) cc_final: 0.8503 (ppp) REVERT: D 430 MET cc_start: 0.8492 (tmm) cc_final: 0.8145 (ttm) REVERT: D 562 MET cc_start: 0.7598 (ttp) cc_final: 0.7303 (ttp) REVERT: D 789 MET cc_start: 0.8766 (mmm) cc_final: 0.8480 (mmt) outliers start: 16 outliers final: 10 residues processed: 269 average time/residue: 0.1252 time to fit residues: 57.4065 Evaluate side-chains 203 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 769 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 134 HIS A 314 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS A 730 HIS B 127 HIS B 616 ASN C 86 GLN C 134 HIS C 314 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 HIS D 127 HIS D 649 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068328 restraints weight = 83800.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070311 restraints weight = 42867.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071620 restraints weight = 28527.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072496 restraints weight = 22231.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072944 restraints weight = 18958.063| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23884 Z= 0.152 Angle : 0.735 10.985 32666 Z= 0.380 Chirality : 0.046 0.260 3928 Planarity : 0.005 0.055 4140 Dihedral : 6.502 60.431 3346 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.20 % Favored : 89.61 % Rotamer: Outliers : 2.48 % Allowed : 14.34 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -2.91 (0.14), residues: 3158 helix: 0.06 (0.14), residues: 1286 sheet: -3.52 (0.22), residues: 412 loop : -3.40 (0.14), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.016 0.001 TYR D 479 PHE 0.029 0.002 PHE D 169 TRP 0.024 0.002 TRP A 813 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (23850) covalent geometry : angle 0.72413 / 0.38 (32582) SS BOND : bond 0.00707 / 0.52 ( 18) SS BOND : angle 2.03102 / 1.55 ( 36) hydrogen bonds : bond 0.04978 / 3.43 ( 1060) hydrogen bonds : angle 5.48348 / 3.91 ( 3102) link_BETA1-4 : bond 0.00601 / 0.30 ( 4) link_BETA1-4 : angle 0.69896 / 0.45 ( 12) link_NAG-ASN : bond 0.00257 / 0.17 ( 12) link_NAG-ASN : angle 3.44970 / 2.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 0.840 Fit side-chains REVERT: A 230 MET cc_start: 0.8641 (mmm) cc_final: 0.8347 (mmm) REVERT: A 269 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8769 (pt) REVERT: A 377 LEU cc_start: 0.8866 (tp) cc_final: 0.8551 (tp) REVERT: A 758 GLU cc_start: 0.8608 (tp30) cc_final: 0.8239 (tm-30) REVERT: A 783 MET cc_start: 0.8102 (mtm) cc_final: 0.7853 (mtp) REVERT: A 789 TRP cc_start: 0.6871 (m-10) cc_final: 0.6669 (m100) REVERT: A 806 MET cc_start: 0.9281 (mmm) cc_final: 0.8508 (mmt) REVERT: B 354 ASP cc_start: 0.8865 (m-30) cc_final: 0.8577 (m-30) REVERT: B 706 MET cc_start: 0.7981 (mtm) cc_final: 0.7763 (mtm) REVERT: C 74 MET cc_start: 0.9039 (tmm) cc_final: 0.8813 (tmm) REVERT: C 230 MET cc_start: 0.8535 (mmm) cc_final: 0.8215 (mmm) REVERT: C 269 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8839 (pt) REVERT: C 347 MET cc_start: 0.9010 (ttp) cc_final: 0.8698 (ttm) REVERT: C 377 LEU cc_start: 0.8781 (tp) cc_final: 0.8423 (tp) REVERT: C 693 LEU cc_start: 0.8900 (tp) cc_final: 0.8487 (tp) REVERT: C 758 GLU cc_start: 0.8764 (tp30) cc_final: 0.8196 (tm-30) REVERT: C 783 MET cc_start: 0.8313 (mtm) cc_final: 0.8046 (mtp) REVERT: C 786 ASP cc_start: 0.6663 (t70) cc_final: 0.6394 (t0) REVERT: C 806 MET cc_start: 0.9204 (mmm) cc_final: 0.8483 (mmt) REVERT: D 132 MET cc_start: 0.8232 (mmm) cc_final: 0.8014 (mmm) REVERT: D 272 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: D 562 MET cc_start: 0.8353 (ttp) cc_final: 0.8091 (ttp) outliers start: 57 outliers final: 25 residues processed: 278 average time/residue: 0.1218 time to fit residues: 58.2436 Evaluate side-chains 227 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 162 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 47 optimal weight: 0.0270 chunk 299 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 294 optimal weight: 40.0000 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.092414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068336 restraints weight = 83446.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070350 restraints weight = 42555.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071667 restraints weight = 28166.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072492 restraints weight = 21862.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073023 restraints weight = 18708.396| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23884 Z= 0.158 Angle : 0.718 11.313 32666 Z= 0.369 Chirality : 0.045 0.250 3928 Planarity : 0.005 0.057 4140 Dihedral : 6.074 60.743 3342 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.13 % Favored : 89.68 % Rotamer: Outliers : 3.49 % Allowed : 15.00 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -2.26 (0.15), residues: 3158 helix: 0.61 (0.14), residues: 1296 sheet: -3.06 (0.23), residues: 442 loop : -3.08 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 694 TYR 0.018 0.001 TYR B 167 PHE 0.022 0.001 PHE B 169 TRP 0.017 0.001 TRP A 813 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (23850) covalent geometry : angle 0.70487 / 0.36 (32582) SS BOND : bond 0.00641 / 0.45 ( 18) SS BOND : angle 2.90517 / 2.09 ( 36) hydrogen bonds : bond 0.04668 / 3.23 ( 1060) hydrogen bonds : angle 5.18891 / 3.70 ( 3102) link_BETA1-4 : bond 0.00189 / 0.09 ( 4) link_BETA1-4 : angle 1.26172 / 0.74 ( 12) link_NAG-ASN : bond 0.00278 / 0.20 ( 12) link_NAG-ASN : angle 3.08440 / 2.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 0.747 Fit side-chains REVERT: A 230 MET cc_start: 0.8622 (mmm) cc_final: 0.8334 (mmm) REVERT: A 269 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8779 (pt) REVERT: A 347 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8669 (ttm) REVERT: A 377 LEU cc_start: 0.8946 (tp) cc_final: 0.8612 (tp) REVERT: A 757 LEU cc_start: 0.8705 (tp) cc_final: 0.8493 (tp) REVERT: A 758 GLU cc_start: 0.8585 (tp30) cc_final: 0.8263 (tm-30) REVERT: A 783 MET cc_start: 0.8129 (mtm) cc_final: 0.7918 (mtp) REVERT: A 806 MET cc_start: 0.9281 (mmm) cc_final: 0.8467 (mmt) REVERT: B 157 MET cc_start: 0.9088 (mtm) cc_final: 0.8618 (mtm) REVERT: B 354 ASP cc_start: 0.8853 (m-30) cc_final: 0.8546 (m-30) REVERT: C 74 MET cc_start: 0.9131 (tmm) cc_final: 0.8860 (tmm) REVERT: C 230 MET cc_start: 0.8539 (mmm) cc_final: 0.8210 (mmm) REVERT: C 269 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8834 (pt) REVERT: C 347 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8692 (ttm) REVERT: C 377 LEU cc_start: 0.8791 (tp) cc_final: 0.8405 (tp) REVERT: C 758 GLU cc_start: 0.8615 (tp30) cc_final: 0.8184 (tm-30) REVERT: C 783 MET cc_start: 0.8290 (mtm) cc_final: 0.8069 (mtp) REVERT: C 786 ASP cc_start: 0.6646 (t70) cc_final: 0.6404 (t0) REVERT: C 806 MET cc_start: 0.9213 (mmm) cc_final: 0.8556 (mmt) REVERT: D 132 MET cc_start: 0.8310 (mmm) cc_final: 0.8063 (mmm) REVERT: D 157 MET cc_start: 0.9013 (mtm) cc_final: 0.8408 (mtm) outliers start: 80 outliers final: 44 residues processed: 278 average time/residue: 0.1244 time to fit residues: 60.2083 Evaluate side-chains 246 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 158 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 311 optimal weight: 0.0570 chunk 300 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 overall best weight: 3.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068257 restraints weight = 83388.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.070239 restraints weight = 42988.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071535 restraints weight = 28656.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072350 restraints weight = 22334.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072864 restraints weight = 19163.999| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23884 Z= 0.168 Angle : 0.702 11.785 32666 Z= 0.359 Chirality : 0.045 0.276 3928 Planarity : 0.005 0.057 4140 Dihedral : 5.745 62.148 3337 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.72 % Favored : 90.15 % Rotamer: Outliers : 3.27 % Allowed : 16.96 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -1.92 (0.15), residues: 3158 helix: 0.94 (0.14), residues: 1284 sheet: -2.82 (0.23), residues: 480 loop : -2.92 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.014 0.001 TYR D 167 PHE 0.026 0.001 PHE B 169 TRP 0.016 0.001 TRP A 813 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (23850) covalent geometry : angle 0.69047 / 0.36 (32582) SS BOND : bond 0.00684 / 0.50 ( 18) SS BOND : angle 2.37318 / 1.77 ( 36) hydrogen bonds : bond 0.04443 / 3.08 ( 1060) hydrogen bonds : angle 4.99366 / 3.57 ( 3102) link_BETA1-4 : bond 0.00272 / 0.14 ( 4) link_BETA1-4 : angle 1.23194 / 0.80 ( 12) link_NAG-ASN : bond 0.00238 / 0.16 ( 12) link_NAG-ASN : angle 3.01018 / 2.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 214 time to evaluate : 0.889 Fit side-chains REVERT: A 230 MET cc_start: 0.8599 (mmm) cc_final: 0.8320 (mmm) REVERT: A 269 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8821 (pt) REVERT: A 347 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8742 (ttm) REVERT: A 377 LEU cc_start: 0.8891 (tp) cc_final: 0.8563 (tp) REVERT: A 757 LEU cc_start: 0.8796 (tp) cc_final: 0.8494 (tp) REVERT: A 758 GLU cc_start: 0.8594 (tp30) cc_final: 0.8297 (tm-30) REVERT: A 806 MET cc_start: 0.9273 (mmm) cc_final: 0.8490 (mmt) REVERT: B 157 MET cc_start: 0.9042 (mtm) cc_final: 0.8593 (mtm) REVERT: B 354 ASP cc_start: 0.8853 (m-30) cc_final: 0.8527 (m-30) REVERT: C 74 MET cc_start: 0.9084 (tmm) cc_final: 0.8766 (tmm) REVERT: C 230 MET cc_start: 0.8525 (mmm) cc_final: 0.8190 (mmm) REVERT: C 269 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8801 (pt) REVERT: C 347 MET cc_start: 0.8989 (ttp) cc_final: 0.8679 (ttm) REVERT: C 375 MET cc_start: 0.8164 (mpp) cc_final: 0.7929 (mpp) REVERT: C 377 LEU cc_start: 0.8875 (tp) cc_final: 0.8485 (tp) REVERT: C 758 GLU cc_start: 0.8689 (tp30) cc_final: 0.8229 (tm-30) REVERT: C 783 MET cc_start: 0.8284 (mtm) cc_final: 0.8083 (mtp) REVERT: C 806 MET cc_start: 0.9207 (mmm) cc_final: 0.8533 (mmt) REVERT: D 101 ASP cc_start: 0.7843 (t0) cc_final: 0.7593 (t0) REVERT: D 132 MET cc_start: 0.8478 (mmm) cc_final: 0.8186 (mmm) outliers start: 75 outliers final: 48 residues processed: 281 average time/residue: 0.1212 time to fit residues: 59.1071 Evaluate side-chains 252 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 691 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.756 > 50: distance: 7 - 13: 26.525 distance: 13 - 14: 55.530 distance: 14 - 15: 41.207 distance: 14 - 17: 29.328 distance: 15 - 21: 57.753 distance: 17 - 18: 11.064 distance: 18 - 19: 50.601 distance: 18 - 20: 47.799 distance: 21 - 22: 34.040 distance: 22 - 23: 31.102 distance: 22 - 25: 46.499 distance: 23 - 24: 9.649 distance: 23 - 30: 19.396 distance: 26 - 27: 20.244 distance: 27 - 28: 30.925 distance: 28 - 29: 39.428 distance: 30 - 31: 47.956 distance: 31 - 32: 21.487 distance: 31 - 34: 27.320 distance: 32 - 33: 32.619 distance: 32 - 38: 31.435 distance: 34 - 35: 33.252 distance: 34 - 36: 21.468 distance: 35 - 37: 41.631 distance: 38 - 39: 7.633 distance: 38 - 212: 27.636 distance: 39 - 40: 11.179 distance: 39 - 42: 34.452 distance: 40 - 41: 30.317 distance: 40 - 45: 59.976 distance: 42 - 43: 20.137 distance: 42 - 44: 41.003 distance: 45 - 46: 14.822 distance: 46 - 47: 44.279 distance: 46 - 49: 22.177 distance: 47 - 48: 20.853 distance: 47 - 52: 39.189 distance: 49 - 50: 10.178 distance: 49 - 51: 24.045 distance: 52 - 53: 28.504 distance: 53 - 54: 28.374 distance: 53 - 56: 59.884 distance: 54 - 55: 4.059 distance: 54 - 60: 53.045 distance: 56 - 57: 39.966 distance: 56 - 58: 46.704 distance: 57 - 59: 20.074 distance: 60 - 61: 5.439 distance: 61 - 62: 33.854 distance: 61 - 64: 53.395 distance: 62 - 63: 39.347 distance: 65 - 66: 20.052 distance: 65 - 67: 40.136 distance: 66 - 68: 44.121 distance: 67 - 69: 34.545 distance: 71 - 72: 60.685 distance: 71 - 74: 40.718 distance: 72 - 73: 43.535 distance: 72 - 79: 17.898 distance: 74 - 75: 57.597 distance: 76 - 77: 48.422 distance: 76 - 78: 47.367 distance: 79 - 80: 20.035 distance: 80 - 81: 28.714 distance: 80 - 83: 65.918 distance: 81 - 82: 14.501 distance: 81 - 84: 51.543 distance: 84 - 85: 41.606 distance: 84 - 90: 49.268 distance: 85 - 86: 49.862 distance: 85 - 88: 46.879 distance: 86 - 87: 39.641 distance: 86 - 91: 34.339 distance: 88 - 89: 35.426 distance: 89 - 90: 31.309