Starting phenix.real_space_refine on Tue Mar 19 05:41:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/03_2024/6whr_21673.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/03_2024/6whr_21673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/03_2024/6whr_21673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/03_2024/6whr_21673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/03_2024/6whr_21673.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/03_2024/6whr_21673.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.684 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 14984 2.51 5 N 3828 2.21 5 O 4428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B GLU 744": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 744": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5870 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 539 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 7, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5717 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 7, 'PHE:plan': 8, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 Chain: "C" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5870 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 539 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 7, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 304 Chain: "D" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5717 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 7, 'PHE:plan': 8, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.11, per 1000 atoms: 0.52 Number of scatterers: 23370 At special positions: 0 Unit cell: (143.85, 149.33, 180.84, 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 4428 8.00 N 3828 7.00 C 14984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.05 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.05 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.05 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 224 " " NAG A1002 " - " ASN A 297 " " NAG B 903 " - " ASN B 542 " " NAG B 904 " - " ASN B 341 " " NAG B 905 " - " ASN B 491 " " NAG C1001 " - " ASN C 224 " " NAG C1002 " - " ASN C 297 " " NAG D 903 " - " ASN D 542 " " NAG D 904 " - " ASN D 341 " " NAG D 905 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 4.3 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 30 sheets defined 41.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.656A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.772A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.965A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.029A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 5.176A pdb=" N MET A 155 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 157 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.668A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.694A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.514A pdb=" N ALA A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.004A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.562A pdb=" N GLU A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.982A pdb=" N TYR A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.373A pdb=" N GLN A 580 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.330A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.895A pdb=" N TRP A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 3.687A pdb=" N ILE A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.608A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) 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 removed outlier: 3.984A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 754 through 764 removed outlier: 5.286A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 removed outlier: 3.517A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 removed outlier: 3.681A pdb=" N ASP A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.813A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.954A pdb=" N LYS B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 4.314A pdb=" N VAL B 64 " --> pdb=" O HIS B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.855A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.876A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.668A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.557A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.986A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 578 removed outlier: 3.619A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 4.311A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.849A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.549A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.637A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.805A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 839 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.657A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.773A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.964A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 143 through 148 removed outlier: 4.028A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 157 removed outlier: 5.176A pdb=" N MET C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 157 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.668A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.694A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.514A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.004A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.563A pdb=" N GLU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.981A pdb=" N TYR C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 548 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 548' Processing helix chain 'C' and resid 576 through 580 removed outlier: 4.372A pdb=" N GLN C 580 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.330A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.896A pdb=" N TRP C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 3.688A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.608A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) 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 removed outlier: 3.983A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 743 Processing helix chain 'C' and resid 754 through 764 removed outlier: 5.287A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 801 removed outlier: 3.517A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 removed outlier: 3.682A pdb=" N ASP C 810 " --> pdb=" O MET C 806 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS C 811 " --> pdb=" O GLU C 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 812 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.813A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.954A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 4.314A pdb=" N VAL D 64 " --> pdb=" O HIS D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.854A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.876A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.668A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 234 through 248 removed outlier: 3.556A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.986A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.619A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 4.311A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 654 Processing helix chain 'D' and resid 668 through 672 Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.851A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.549A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.637A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D 793 " --> pdb=" O MET D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.805A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D 838 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 839 " --> pdb=" O THR D 835 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.449A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 6.445A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 7.357A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.773A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 4.433A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 753 removed outlier: 3.631A pdb=" N VAL A 563 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 768 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.631A pdb=" N ILE B 37 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 204 removed outlier: 8.097A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.882A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AB3, first strand: chain 'B' and resid 475 through 477 removed outlier: 8.964A pdb=" N MET B 508 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB6, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.853A pdb=" N ALA B 728 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.448A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 removed outlier: 6.445A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 288 through 292 removed outlier: 7.356A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 422 through 423 removed outlier: 3.773A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 434 Processing sheet with id=AC3, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.434A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 750 through 753 removed outlier: 3.631A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.631A pdb=" N ILE D 37 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 199 through 204 removed outlier: 8.098A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 278 through 280 removed outlier: 6.882A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 341 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 475 through 477 removed outlier: 8.964A pdb=" N MET D 508 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER D 407 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 419 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.854A pdb=" N ALA D 728 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2658 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: 6.92 Time building geometry restraints manager: 10.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6131 1.33 - 1.46: 6905 1.46 - 1.59: 10604 1.59 - 1.72: 0 1.72 - 1.85: 218 Bond restraints: 23858 Sorted by residual: bond pdb=" CA ALA A 755 " pdb=" C ALA A 755 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.79e+01 bond pdb=" CA ALA C 755 " pdb=" C ALA C 755 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.75e+01 bond pdb=" CA SER D 520 " pdb=" C SER D 520 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.34e-02 5.57e+03 4.43e+01 bond pdb=" CA SER B 520 " pdb=" C SER B 520 " ideal model delta sigma weight residual 1.523 1.435 0.089 1.34e-02 5.57e+03 4.37e+01 bond pdb=" CA MET B 789 " pdb=" C MET B 789 " ideal model delta sigma weight residual 1.524 1.404 0.120 2.25e-02 1.98e+03 2.83e+01 ... (remaining 23853 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.65: 439 104.65 - 112.05: 12775 112.05 - 119.44: 7627 119.44 - 126.83: 11445 126.83 - 134.23: 300 Bond angle restraints: 32586 Sorted by residual: angle pdb=" C LYS D 747 " pdb=" N LEU D 748 " pdb=" CA LEU D 748 " ideal model delta sigma weight residual 121.64 114.05 7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" C LYS B 747 " pdb=" N LEU B 748 " pdb=" CA LEU B 748 " ideal model delta sigma weight residual 121.64 114.09 7.55 1.20e+00 6.94e-01 3.96e+01 angle pdb=" C PHE D 529 " pdb=" CA PHE D 529 " pdb=" CB PHE D 529 " ideal model delta sigma weight residual 111.39 103.02 8.37 1.59e+00 3.96e-01 2.77e+01 angle pdb=" C PHE B 529 " pdb=" CA PHE B 529 " pdb=" CB PHE B 529 " ideal model delta sigma weight residual 111.39 103.07 8.32 1.59e+00 3.96e-01 2.73e+01 angle pdb=" C LEU C 676 " pdb=" N VAL C 677 " pdb=" CA VAL C 677 " ideal model delta sigma weight residual 122.35 116.84 5.51 1.18e+00 7.18e-01 2.18e+01 ... (remaining 32581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 13125 22.27 - 44.54: 897 44.54 - 66.81: 158 66.81 - 89.07: 36 89.07 - 111.34: 40 Dihedral angle restraints: 14256 sinusoidal: 5096 harmonic: 9160 Sorted by residual: dihedral pdb=" CA CYS D 429 " pdb=" C CYS D 429 " pdb=" N MET D 430 " pdb=" CA MET D 430 " ideal model delta harmonic sigma weight residual 180.00 132.00 48.00 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA CYS B 429 " pdb=" C CYS B 429 " pdb=" N MET B 430 " pdb=" CA MET B 430 " ideal model delta harmonic sigma weight residual 180.00 132.06 47.94 0 5.00e+00 4.00e-02 9.19e+01 dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -165.58 79.58 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 14253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3910 0.321 - 0.643: 2 0.643 - 0.964: 0 0.964 - 1.286: 0 1.286 - 1.607: 2 Chirality restraints: 3914 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 -0.79 -1.61 2.00e-02 2.50e+03 6.46e+03 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 -0.79 -1.61 2.00e-02 2.50e+03 6.45e+03 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 224 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.03e+00 ... (remaining 3911 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 632 " -0.023 2.00e-02 2.50e+03 1.52e-02 5.81e+00 pdb=" CG TRP A 632 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 632 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 632 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 632 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 632 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 632 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 632 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 632 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 632 " 0.023 2.00e-02 2.50e+03 1.52e-02 5.81e+00 pdb=" CG TRP C 632 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 632 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 632 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 632 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 632 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 632 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 632 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 632 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 547 " 0.001 2.00e-02 2.50e+03 1.61e-02 5.17e+00 pdb=" CG TYR C 547 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 547 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 547 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 547 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 547 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 547 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 547 " -0.003 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 497 2.55 - 3.14: 24171 3.14 - 3.73: 35745 3.73 - 4.31: 46420 4.31 - 4.90: 70640 Nonbonded interactions: 177473 Sorted by model distance: nonbonded pdb=" OG1 THR A 446 " pdb=" OD1 ASN A 448 " model vdw 1.968 2.440 nonbonded pdb=" OG1 THR C 446 " pdb=" OD1 ASN C 448 " model vdw 1.968 2.440 nonbonded pdb=" O LYS A 706 " pdb=" OG SER A 708 " model vdw 2.049 2.440 nonbonded pdb=" O LYS C 706 " pdb=" OG SER C 708 " model vdw 2.049 2.440 nonbonded pdb=" N ASP C 753 " pdb=" OD1 ASP C 753 " model vdw 2.050 2.520 ... (remaining 177468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.700 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: 0.020 Extract box with map and model: 5.100 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 60.110 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 71.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.015 0.120 23858 Z= 0.999 Angle : 1.228 13.288 32586 Z= 0.661 Chirality : 0.071 1.607 3914 Planarity : 0.006 0.053 4132 Dihedral : 17.345 111.343 8296 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 30.82 Ramachandran Plot: Outliers : 0.83 % Allowed : 21.19 % Favored : 77.98 % Rotamer: Outliers : 2.94 % Allowed : 16.88 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.11), residues: 3138 helix: -3.34 (0.11), residues: 1132 sheet: -4.08 (0.19), residues: 370 loop : -4.43 (0.12), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 632 HIS 0.017 0.004 HIS C 162 PHE 0.031 0.004 PHE B 729 TYR 0.034 0.003 TYR C 547 ARG 0.006 0.001 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 605 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7567 (t) REVERT: A 662 MET cc_start: 0.8307 (tmm) cc_final: 0.8019 (tmm) REVERT: A 686 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8104 (p) REVERT: B 548 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.7576 (p) REVERT: B 818 MET cc_start: 0.6837 (mmm) cc_final: 0.6215 (mmp) REVERT: C 349 SER cc_start: 0.6011 (OUTLIER) cc_final: 0.5720 (p) REVERT: C 575 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 605 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.6821 (t) REVERT: C 686 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (p) REVERT: D 654 MET cc_start: 0.7862 (mmt) cc_final: 0.7612 (tpp) REVERT: D 818 MET cc_start: 0.6846 (mmm) cc_final: 0.6166 (mmt) outliers start: 68 outliers final: 47 residues processed: 262 average time/residue: 0.2643 time to fit residues: 119.0582 Evaluate side-chains 226 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 483 ASN Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 760 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 160 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 577 GLN A 731 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS C 384 GLN C 577 GLN ** C 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 23858 Z= 0.378 Angle : 0.801 10.822 32586 Z= 0.415 Chirality : 0.049 0.456 3914 Planarity : 0.005 0.052 4132 Dihedral : 13.713 102.349 3694 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.73 % Favored : 88.08 % Rotamer: Outliers : 5.87 % Allowed : 20.47 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.13), residues: 3138 helix: -1.70 (0.13), residues: 1182 sheet: -3.38 (0.22), residues: 368 loop : -3.80 (0.13), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 607 HIS 0.011 0.001 HIS C 162 PHE 0.041 0.002 PHE C 42 TYR 0.028 0.002 TYR C 547 ARG 0.005 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 209 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 662 MET cc_start: 0.8072 (tmm) cc_final: 0.7830 (tmm) REVERT: A 789 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6794 (p-90) REVERT: B 334 MET cc_start: 0.6952 (mmm) cc_final: 0.6330 (mmp) REVERT: B 548 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7134 (p) REVERT: B 554 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5949 (m-10) REVERT: B 566 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6604 (mp) REVERT: B 654 MET cc_start: 0.7811 (mmp) cc_final: 0.7522 (mmt) REVERT: B 818 MET cc_start: 0.6362 (mmm) cc_final: 0.5944 (mmp) REVERT: B 829 MET cc_start: 0.6286 (mpp) cc_final: 0.5077 (mtm) REVERT: C 575 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6847 (t80) REVERT: C 789 TRP cc_start: 0.7723 (OUTLIER) cc_final: 0.6965 (p-90) REVERT: D 554 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5945 (m-10) REVERT: D 654 MET cc_start: 0.7706 (mmt) cc_final: 0.7345 (tpp) REVERT: D 797 LEU cc_start: 0.8352 (mt) cc_final: 0.7985 (mp) REVERT: D 818 MET cc_start: 0.6567 (mmm) cc_final: 0.5860 (mmp) outliers start: 136 outliers final: 86 residues processed: 332 average time/residue: 0.2703 time to fit residues: 154.0263 Evaluate side-chains 276 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 182 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 786 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 237 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 229 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 HIS B 152 GLN C 278 ASN C 748 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23858 Z= 0.253 Angle : 0.701 10.349 32586 Z= 0.359 Chirality : 0.047 0.425 3914 Planarity : 0.004 0.055 4132 Dihedral : 11.292 94.406 3671 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.96 % Favored : 88.85 % Rotamer: Outliers : 5.96 % Allowed : 22.71 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.14), residues: 3138 helix: -0.50 (0.14), residues: 1194 sheet: -3.00 (0.24), residues: 350 loop : -3.38 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 519 HIS 0.009 0.001 HIS A 162 PHE 0.015 0.001 PHE D 677 TYR 0.020 0.002 TYR C 109 ARG 0.002 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 207 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6602 (t80) REVERT: B 257 ILE cc_start: 0.6993 (mp) cc_final: 0.6661 (mt) REVERT: B 452 TYR cc_start: 0.5291 (t80) cc_final: 0.5062 (t80) REVERT: B 566 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6558 (mp) REVERT: B 654 MET cc_start: 0.7764 (mmp) cc_final: 0.7536 (tpp) REVERT: B 797 LEU cc_start: 0.8335 (mt) cc_final: 0.8072 (mp) REVERT: B 818 MET cc_start: 0.6176 (mmm) cc_final: 0.5859 (mmp) REVERT: C 575 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6793 (t80) REVERT: D 257 ILE cc_start: 0.6764 (mp) cc_final: 0.6526 (mt) REVERT: D 339 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6578 (mm) REVERT: D 566 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6304 (mp) REVERT: D 654 MET cc_start: 0.7466 (mmt) cc_final: 0.7115 (tpp) REVERT: D 797 LEU cc_start: 0.8313 (mt) cc_final: 0.7982 (mp) REVERT: D 818 MET cc_start: 0.6294 (mmm) cc_final: 0.5656 (mmp) REVERT: D 829 MET cc_start: 0.6106 (mpp) cc_final: 0.4997 (mtm) outliers start: 138 outliers final: 93 residues processed: 327 average time/residue: 0.2637 time to fit residues: 147.7174 Evaluate side-chains 289 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 191 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 784 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 148 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 278 ASN A 801 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN C 731 ASN D 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23858 Z= 0.200 Angle : 0.675 10.507 32586 Z= 0.342 Chirality : 0.047 0.421 3914 Planarity : 0.004 0.053 4132 Dihedral : 9.787 85.219 3658 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.66 % Favored : 90.15 % Rotamer: Outliers : 5.27 % Allowed : 23.58 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.14), residues: 3138 helix: 0.15 (0.15), residues: 1178 sheet: -2.73 (0.24), residues: 356 loop : -3.21 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 607 HIS 0.008 0.001 HIS A 162 PHE 0.016 0.001 PHE B 677 TYR 0.018 0.001 TYR C 351 ARG 0.004 0.000 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 203 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5374 (mm) REVERT: A 575 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 783 MET cc_start: 0.7354 (tpp) cc_final: 0.7071 (tpp) REVERT: A 789 TRP cc_start: 0.7501 (OUTLIER) cc_final: 0.6523 (p-90) REVERT: B 566 LEU cc_start: 0.6808 (mt) cc_final: 0.6593 (mp) REVERT: B 654 MET cc_start: 0.7619 (mmp) cc_final: 0.7389 (tpp) REVERT: B 716 ASP cc_start: 0.5143 (m-30) cc_final: 0.4823 (m-30) REVERT: B 797 LEU cc_start: 0.8274 (mt) cc_final: 0.8018 (mp) REVERT: B 818 MET cc_start: 0.5926 (mmm) cc_final: 0.5620 (mmp) REVERT: B 829 MET cc_start: 0.5999 (mpp) cc_final: 0.4392 (mtm) REVERT: C 91 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5330 (mm) REVERT: C 575 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6669 (t80) REVERT: C 783 MET cc_start: 0.7218 (tpp) cc_final: 0.6983 (tpp) REVERT: C 789 TRP cc_start: 0.7559 (OUTLIER) cc_final: 0.6597 (p-90) REVERT: D 412 GLU cc_start: 0.7405 (tp30) cc_final: 0.6769 (tp30) REVERT: D 797 LEU cc_start: 0.8245 (mt) cc_final: 0.7932 (mp) REVERT: D 818 MET cc_start: 0.5962 (mmm) cc_final: 0.5510 (mmp) REVERT: D 829 MET cc_start: 0.5712 (mpp) cc_final: 0.4568 (mtm) outliers start: 122 outliers final: 89 residues processed: 310 average time/residue: 0.2710 time to fit residues: 144.8159 Evaluate side-chains 284 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 189 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 PHE Chi-restraints excluded: chain A residue 599 TYR Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 PHE Chi-restraints excluded: chain C residue 599 TYR Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 789 TRP Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 757 PHE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 784 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2399 > 50: distance: 20 - 23: 6.836 distance: 23 - 24: 4.955 distance: 24 - 25: 4.439 distance: 24 - 27: 18.642 distance: 25 - 26: 4.014 distance: 25 - 29: 6.645 distance: 27 - 28: 19.004 distance: 29 - 30: 9.071 distance: 30 - 31: 15.294 distance: 30 - 33: 5.951 distance: 31 - 32: 22.882 distance: 31 - 37: 24.795 distance: 33 - 34: 11.781 distance: 34 - 35: 8.810 distance: 34 - 36: 6.520 distance: 37 - 38: 42.263 distance: 38 - 39: 20.730 distance: 38 - 41: 21.478 distance: 39 - 40: 26.070 distance: 39 - 42: 3.506 distance: 42 - 43: 8.603 distance: 42 - 48: 13.706 distance: 43 - 44: 3.068 distance: 43 - 46: 8.855 distance: 44 - 45: 20.247 distance: 44 - 49: 9.403 distance: 46 - 47: 17.569 distance: 47 - 48: 8.539 distance: 49 - 50: 10.649 distance: 50 - 51: 6.182 distance: 50 - 53: 5.834 distance: 51 - 52: 4.083 distance: 51 - 54: 8.714 distance: 54 - 55: 6.016 distance: 55 - 56: 7.131 distance: 55 - 58: 7.440 distance: 56 - 57: 10.446 distance: 56 - 61: 6.723 distance: 58 - 59: 7.720 distance: 58 - 60: 5.151 distance: 62 - 63: 6.347 distance: 62 - 65: 4.224 distance: 63 - 64: 5.844 distance: 63 - 69: 3.857 distance: 65 - 66: 7.807 distance: 66 - 67: 13.026 distance: 66 - 68: 12.522 distance: 69 - 70: 14.318 distance: 70 - 71: 11.873 distance: 70 - 73: 3.161 distance: 71 - 72: 11.614 distance: 71 - 76: 12.144 distance: 73 - 74: 7.565 distance: 73 - 75: 10.307 distance: 76 - 77: 20.346 distance: 77 - 78: 14.628 distance: 77 - 80: 19.761 distance: 78 - 79: 11.571 distance: 78 - 82: 8.801 distance: 80 - 81: 7.131 distance: 81 - 124: 5.641 distance: 82 - 83: 10.082 distance: 83 - 84: 4.785 distance: 83 - 86: 11.446 distance: 84 - 85: 14.410 distance: 84 - 87: 8.637