Starting phenix.real_space_refine on Sun Aug 24 23:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6why_21680/08_2025/6why_21680.cif Found real_map, /net/cci-nas-00/data/ceres_data/6why_21680/08_2025/6why_21680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6why_21680/08_2025/6why_21680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6why_21680/08_2025/6why_21680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6why_21680/08_2025/6why_21680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6why_21680/08_2025/6why_21680.map" } resolution = 4.03 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= 0.017 sd= 0.833 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2138 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 Cl 4 4.86 5 C 14284 2.51 5 N 3626 2.21 5 O 4158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22198 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 5608 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 33, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 785 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 11, 'ARG:plan': 27, 'GLN:plan1': 11, 'PHE:plan': 5, 'TYR:plan': 3, 'HIS:plan': 6, 'ASP:plan': 14, 'GLU:plan': 26} Unresolved non-hydrogen planarities: 439 Chain: "B" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5424 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 26, 'TRANS': 732} Chain breaks: 5 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 734 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 5, 'GLU:plan': 27, 'ASN:plan1': 6, 'ARG:plan': 13, 'GLN:plan1': 13, 'TYR:plan': 10, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 404 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: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D, F Time building chain proxies: 7.57, per 1000 atoms: 0.34 Number of scatterers: 22198 At special positions: 0 Unit cell: (141.11, 147.96, 182.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 126 16.00 O 4158 8.00 N 3626 7.00 C 14284 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.03 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 557 " - pdb=" SG CYS C 831 " distance=2.01 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=2.04 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=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 903 " - " ASN B 542 " " NAG D 903 " - " ASN D 542 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 792.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5792 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 34 sheets defined 43.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 71 through 82 removed outlier: 4.748A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.327A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.521A pdb=" N MET A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.974A pdb=" N THR A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.570A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.654A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 removed outlier: 4.208A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.668A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.658A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 604 removed outlier: 4.096A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.660A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 4.011A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 659 " --> pdb=" O MET A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.747A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 removed outlier: 4.899A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.908A pdb=" N GLU A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.509A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 52 through 60 removed outlier: 4.219A pdb=" N LYS B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.043A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 215 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.143A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.742A pdb=" N VAL B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 263 " --> pdb=" O SER B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.973A pdb=" N ASP B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.576A pdb=" N HIS B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.510A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.310A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 4.495A pdb=" N PHE B 550 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 578 removed outlier: 4.642A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 614 removed outlier: 3.915A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 651 removed outlier: 3.504A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.936A pdb=" N GLN B 656 " --> pdb=" O PHE B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 691 No H-bonds generated for 'chain 'B' and resid 689 through 691' Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 700 through 707 removed outlier: 4.067A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.511A pdb=" N THR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 772 through 784 removed outlier: 3.590A pdb=" N ASP B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 818 through 844 removed outlier: 3.882A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.748A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.327A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.521A pdb=" N MET C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.974A pdb=" N THR C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 298 through 314 removed outlier: 3.569A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 4.654A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 removed outlier: 4.208A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.668A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 removed outlier: 3.659A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 604 removed outlier: 4.097A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.660A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 4.011A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 710 through 715 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.748A pdb=" N ILE C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 762 removed outlier: 4.899A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 removed outlier: 3.908A pdb=" N GLU C 802 " --> pdb=" O LEU C 798 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN C 803 " --> pdb=" O LYS C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'C' and resid 835 through 861 removed outlier: 3.508A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 52 through 60 removed outlier: 4.218A pdb=" N LYS D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 106 through 120 removed outlier: 4.043A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 215 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.143A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.741A pdb=" N VAL D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 263 " --> pdb=" O SER D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.973A pdb=" N ASP D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 removed outlier: 3.577A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 removed outlier: 3.511A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.311A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 523 " --> pdb=" O ARG D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 removed outlier: 4.495A pdb=" N PHE D 550 " --> pdb=" O PRO D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 578 removed outlier: 4.642A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 614 removed outlier: 3.915A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 651 removed outlier: 3.505A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 656 removed outlier: 3.935A pdb=" N GLN D 656 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 691 No H-bonds generated for 'chain 'D' and resid 689 through 691' Processing helix chain 'D' and resid 692 through 697 Processing helix chain 'D' and resid 700 through 707 removed outlier: 4.067A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 removed outlier: 3.511A pdb=" N THR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 772 through 784 removed outlier: 3.590A pdb=" N ASP D 777 " --> pdb=" O LYS D 773 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 818 through 844 removed outlier: 3.883A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 65 removed outlier: 3.796A pdb=" N GLN A 61 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 218 removed outlier: 5.973A pdb=" N ILE A 163 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 214 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 165 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 241 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A 168 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 292 removed outlier: 4.049A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.354A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 538 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY A 778 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 538 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY A 778 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 777 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 555 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 511 Processing sheet with id=AA9, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.697A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY B 125 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.615A pdb=" N PHE B 169 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 202 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 171 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B 173 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 172 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 405 through 406 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 417 through 420 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 683 through 684 removed outlier: 6.432A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.432A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 60 through 65 removed outlier: 3.796A pdb=" N GLN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 211 through 218 removed outlier: 5.973A pdb=" N ILE C 163 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS C 214 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 165 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 241 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 168 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 291 through 292 removed outlier: 4.047A pdb=" N GLY C 386 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.354A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 538 " --> pdb=" O GLY C 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY C 778 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 497 through 499 removed outlier: 6.451A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 538 " --> pdb=" O GLY C 778 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY C 778 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 777 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS C 555 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC7, first strand: chain 'C' and resid 508 through 511 Processing sheet with id=AC8, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AC9, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.696A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY D 125 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.615A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 172 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 405 through 406 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 417 through 420 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 683 through 684 removed outlier: 6.432A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.432A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 934 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3670 1.31 - 1.44: 6017 1.44 - 1.57: 12767 1.57 - 1.70: 0 1.70 - 1.83: 214 Bond restraints: 22668 Sorted by residual: bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.472 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.472 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" ND2 QGM A1001 " pdb=" CAR QGM A1001 " ideal model delta sigma weight residual 1.354 1.454 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" ND2 QGM C1001 " pdb=" CAR QGM C1001 " ideal model delta sigma weight residual 1.354 1.454 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CAR QGM A1001 " pdb=" NAN QGM A1001 " ideal model delta sigma weight residual 1.376 1.455 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 22663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 30665 2.85 - 5.70: 349 5.70 - 8.55: 44 8.55 - 11.39: 2 11.39 - 14.24: 2 Bond angle restraints: 31062 Sorted by residual: angle pdb=" N GLN C 791 " pdb=" CA GLN C 791 " pdb=" C GLN C 791 " ideal model delta sigma weight residual 111.28 104.55 6.73 1.09e+00 8.42e-01 3.81e+01 angle pdb=" N GLN A 791 " pdb=" CA GLN A 791 " pdb=" C GLN A 791 " ideal model delta sigma weight residual 111.28 104.58 6.70 1.09e+00 8.42e-01 3.77e+01 angle pdb=" C ASP D 661 " pdb=" N GLN D 662 " pdb=" CA GLN D 662 " ideal model delta sigma weight residual 121.90 114.25 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C ASP B 661 " pdb=" N GLN B 662 " pdb=" CA GLN B 662 " ideal model delta sigma weight residual 121.90 114.26 7.64 1.26e+00 6.30e-01 3.68e+01 angle pdb=" O LYS C 790 " pdb=" C LYS C 790 " pdb=" N GLN C 791 " ideal model delta sigma weight residual 122.08 128.20 -6.12 1.07e+00 8.73e-01 3.27e+01 ... (remaining 31057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 12358 21.45 - 42.90: 744 42.90 - 64.35: 142 64.35 - 85.80: 52 85.80 - 107.26: 24 Dihedral angle restraints: 13320 sinusoidal: 4366 harmonic: 8954 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 329 " pdb=" CB CYS C 329 " ideal model delta sinusoidal sigma weight residual 93.00 30.94 62.06 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual 93.00 30.95 62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 150.05 -57.05 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 13317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 3792 0.303 - 0.606: 2 0.606 - 0.909: 0 0.909 - 1.211: 0 1.211 - 1.514: 2 Chirality restraints: 3796 Sorted by residual: 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 -0.89 -1.51 2.00e-02 2.50e+03 5.73e+03 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 -0.89 -1.51 2.00e-02 2.50e+03 5.73e+03 chirality pdb=" CG QGM A1001 " pdb=" CB QGM A1001 " pdb=" CD1 QGM A1001 " pdb=" ND2 QGM A1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 3793 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 792 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C GLN A 792 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 792 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 793 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 792 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN C 792 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN C 792 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 793 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 791 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C GLN A 791 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 791 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 792 " 0.012 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1107 2.70 - 3.25: 24779 3.25 - 3.80: 34053 3.80 - 4.35: 39907 4.35 - 4.90: 63555 Nonbonded interactions: 163401 Sorted by model distance: nonbonded pdb=" O ASP C 248 " pdb=" OG1 THR C 251 " model vdw 2.150 3.040 nonbonded pdb=" O ASP A 248 " pdb=" OG1 THR A 251 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR C 446 " pdb=" OD1 ASP C 450 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" OD1 ASP A 450 " model vdw 2.155 3.040 nonbonded pdb=" O LEU A 487 " pdb=" OG1 THR A 490 " model vdw 2.158 3.040 ... (remaining 163396 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: 0.04 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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 : 0.006 0.125 22694 Z= 0.283 Angle : 1.012 52.011 31116 Z= 0.514 Chirality : 0.059 1.514 3796 Planarity : 0.005 0.047 3930 Dihedral : 16.278 107.256 7474 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 1.71 % Allowed : 8.44 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.12 (0.12), residues: 3054 helix: -2.89 (0.12), residues: 1128 sheet: -3.46 (0.21), residues: 334 loop : -3.86 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 380 TYR 0.024 0.002 TYR A 128 PHE 0.015 0.002 PHE C 630 TRP 0.017 0.002 TRP A 789 HIS 0.007 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00567 (22668) covalent geometry : angle 0.83408 (31062) SS BOND : bond 0.00811 ( 18) SS BOND : angle 1.89578 ( 36) hydrogen bonds : bond 0.17478 ( 926) hydrogen bonds : angle 8.05952 ( 2664) Misc. bond : bond 0.00029 ( 2) link_BETA1-4 : bond 0.06470 ( 2) link_BETA1-4 : angle 40.97723 ( 6) link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 1.68962 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6381 (tpp) cc_final: 0.5973 (tpt) REVERT: A 597 MET cc_start: 0.7153 (ttt) cc_final: 0.6549 (ttt) REVERT: B 366 LEU cc_start: 0.5065 (tp) cc_final: 0.4855 (tp) REVERT: B 426 SER cc_start: 0.4249 (OUTLIER) cc_final: 0.4010 (m) REVERT: C 154 MET cc_start: 0.5906 (tpp) cc_final: 0.4804 (tpt) REVERT: C 486 LYS cc_start: 0.8291 (tmtt) cc_final: 0.8080 (tptp) REVERT: D 37 ILE cc_start: 0.6326 (mp) cc_final: 0.6003 (mt) REVERT: D 188 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7470 (t) REVERT: D 258 VAL cc_start: 0.6875 (m) cc_final: 0.6571 (m) REVERT: D 426 SER cc_start: 0.5455 (OUTLIER) cc_final: 0.4854 (m) REVERT: D 809 MET cc_start: 0.8685 (tmm) cc_final: 0.8419 (tmm) outliers start: 36 outliers final: 17 residues processed: 324 average time/residue: 0.1013 time to fit residues: 55.4810 Evaluate side-chains 234 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 73 GLN A 134 HIS A 146 HIS A 291 GLN A 371 GLN A 592 HIS B 110 GLN B 159 ASN B 621 GLN C 38 HIS C 70 ASN C 73 GLN C 134 HIS C 146 HIS C 291 GLN C 371 GLN C 498 HIS C 542 ASN C 592 HIS D 110 GLN D 621 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.107330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089213 restraints weight = 89059.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088545 restraints weight = 54114.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.089331 restraints weight = 51612.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.089584 restraints weight = 40706.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.089713 restraints weight = 38584.778| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22694 Z= 0.181 Angle : 0.727 9.607 31116 Z= 0.379 Chirality : 0.048 0.291 3796 Planarity : 0.005 0.041 3930 Dihedral : 10.265 89.480 3376 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.13), residues: 3054 helix: -1.46 (0.14), residues: 1184 sheet: -3.06 (0.22), residues: 332 loop : -3.29 (0.14), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 716 TYR 0.019 0.001 TYR C 128 PHE 0.022 0.002 PHE A 805 TRP 0.015 0.002 TRP A 789 HIS 0.006 0.001 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.00406 (22668) covalent geometry : angle 0.72505 (31062) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.35577 ( 36) hydrogen bonds : bond 0.04661 ( 926) hydrogen bonds : angle 6.38994 ( 2664) Misc. bond : bond 0.00470 ( 2) link_BETA1-4 : bond 0.00739 ( 2) link_BETA1-4 : angle 1.89905 ( 6) link_NAG-ASN : bond 0.00531 ( 4) link_NAG-ASN : angle 1.27771 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LYS cc_start: 0.9446 (tmtt) cc_final: 0.9236 (ttmt) REVERT: A 720 LEU cc_start: 0.8736 (mt) cc_final: 0.8074 (mt) REVERT: B 609 LEU cc_start: 0.9217 (mm) cc_final: 0.8952 (tt) REVERT: C 486 LYS cc_start: 0.9519 (tmtt) cc_final: 0.9249 (ttmt) REVERT: C 491 MET cc_start: 0.8734 (mtp) cc_final: 0.8532 (mtp) REVERT: C 655 MET cc_start: 0.7055 (mtp) cc_final: 0.6820 (ttp) REVERT: C 720 LEU cc_start: 0.8841 (mt) cc_final: 0.8313 (mt) REVERT: D 336 ASN cc_start: 0.8804 (p0) cc_final: 0.8371 (p0) REVERT: D 561 MET cc_start: 0.9016 (ttm) cc_final: 0.8546 (ttm) REVERT: D 742 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8162 (tmm-80) REVERT: D 809 MET cc_start: 0.8664 (tmm) cc_final: 0.8289 (tmm) outliers start: 2 outliers final: 0 residues processed: 298 average time/residue: 0.1050 time to fit residues: 53.7497 Evaluate side-chains 228 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 206 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 255 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 672 GLN B 840 HIS D 616 ASN D 672 GLN D 840 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.109027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.090910 restraints weight = 88826.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.090192 restraints weight = 53888.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091042 restraints weight = 50534.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091528 restraints weight = 39467.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091635 restraints weight = 36711.154| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22694 Z= 0.151 Angle : 0.665 10.670 31116 Z= 0.348 Chirality : 0.046 0.264 3796 Planarity : 0.004 0.052 3930 Dihedral : 8.836 83.551 3376 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.14), residues: 3054 helix: -0.65 (0.15), residues: 1186 sheet: -2.65 (0.24), residues: 354 loop : -3.09 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 693 TYR 0.020 0.001 TYR C 128 PHE 0.027 0.002 PHE B 144 TRP 0.015 0.001 TRP C 789 HIS 0.005 0.001 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.00338 (22668) covalent geometry : angle 0.66257 (31062) SS BOND : bond 0.00670 ( 18) SS BOND : angle 1.30815 ( 36) hydrogen bonds : bond 0.04089 ( 926) hydrogen bonds : angle 5.88472 ( 2664) Misc. bond : bond 0.00061 ( 2) link_BETA1-4 : bond 0.01049 ( 2) link_BETA1-4 : angle 2.27909 ( 6) link_NAG-ASN : bond 0.00377 ( 4) link_NAG-ASN : angle 1.25602 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8107 (ptm) cc_final: 0.7895 (ptt) REVERT: A 597 MET cc_start: 0.9068 (ttm) cc_final: 0.8455 (ttm) REVERT: B 59 PHE cc_start: 0.7403 (m-80) cc_final: 0.7138 (m-80) REVERT: B 161 MET cc_start: 0.5249 (mtp) cc_final: 0.4721 (ttm) REVERT: B 230 LEU cc_start: 0.7869 (tp) cc_final: 0.7584 (mt) REVERT: B 285 TRP cc_start: 0.8021 (m100) cc_final: 0.7211 (m100) REVERT: B 508 MET cc_start: 0.7910 (ttp) cc_final: 0.7647 (ttp) REVERT: B 702 MET cc_start: 0.9090 (mtt) cc_final: 0.8702 (mtm) REVERT: B 829 MET cc_start: 0.8945 (mtp) cc_final: 0.8589 (mtp) REVERT: D 126 ILE cc_start: 0.9231 (pt) cc_final: 0.8900 (mm) REVERT: D 702 MET cc_start: 0.9008 (mtt) cc_final: 0.8589 (mtm) REVERT: D 809 MET cc_start: 0.8562 (tmm) cc_final: 0.8277 (tmm) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.0978 time to fit residues: 49.8028 Evaluate side-chains 229 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 168 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.111573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.093657 restraints weight = 87636.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.092833 restraints weight = 51441.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.093839 restraints weight = 47008.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.094561 restraints weight = 36184.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.094777 restraints weight = 32921.055| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22694 Z= 0.117 Angle : 0.634 11.220 31116 Z= 0.328 Chirality : 0.045 0.256 3796 Planarity : 0.004 0.041 3930 Dihedral : 8.050 77.778 3376 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 3054 helix: -0.11 (0.15), residues: 1182 sheet: -2.35 (0.25), residues: 358 loop : -2.85 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 742 TYR 0.016 0.001 TYR A 128 PHE 0.024 0.001 PHE D 653 TRP 0.018 0.001 TRP B 610 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00258 (22668) covalent geometry : angle 0.63116 (31062) SS BOND : bond 0.00502 ( 18) SS BOND : angle 1.22283 ( 36) hydrogen bonds : bond 0.03598 ( 926) hydrogen bonds : angle 5.47430 ( 2664) Misc. bond : bond 0.00023 ( 2) link_BETA1-4 : bond 0.01279 ( 2) link_BETA1-4 : angle 3.03716 ( 6) link_NAG-ASN : bond 0.00410 ( 4) link_NAG-ASN : angle 0.95723 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8288 (tp30) cc_final: 0.8068 (tp30) REVERT: A 491 MET cc_start: 0.8638 (mtp) cc_final: 0.8111 (mtm) REVERT: A 597 MET cc_start: 0.9167 (ttm) cc_final: 0.8605 (ttm) REVERT: A 652 ILE cc_start: 0.9130 (tp) cc_final: 0.8910 (tp) REVERT: A 655 MET cc_start: 0.8169 (tpt) cc_final: 0.7863 (mmm) REVERT: B 59 PHE cc_start: 0.7526 (m-80) cc_final: 0.7131 (m-10) REVERT: B 285 TRP cc_start: 0.7916 (m100) cc_final: 0.7150 (m100) REVERT: B 561 MET cc_start: 0.8960 (ttm) cc_final: 0.8655 (ttm) REVERT: B 654 MET cc_start: 0.8534 (mtp) cc_final: 0.8240 (mtp) REVERT: B 702 MET cc_start: 0.9073 (mtt) cc_final: 0.8862 (mtm) REVERT: B 829 MET cc_start: 0.8946 (mtp) cc_final: 0.8607 (mtp) REVERT: D 126 ILE cc_start: 0.9296 (pt) cc_final: 0.8997 (mm) REVERT: D 498 ILE cc_start: 0.9142 (mm) cc_final: 0.8914 (mm) REVERT: D 561 MET cc_start: 0.9095 (ttm) cc_final: 0.8591 (ttm) REVERT: D 702 MET cc_start: 0.8771 (mtt) cc_final: 0.8495 (mtm) REVERT: D 809 MET cc_start: 0.8380 (tmm) cc_final: 0.8113 (tmm) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.0953 time to fit residues: 52.1754 Evaluate side-chains 241 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 234 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 249 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 50 ASN B 775 GLN D 775 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.115425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.096505 restraints weight = 88008.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.097421 restraints weight = 47635.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097861 restraints weight = 36536.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098160 restraints weight = 32797.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098563 restraints weight = 30140.679| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22694 Z= 0.114 Angle : 0.614 9.106 31116 Z= 0.316 Chirality : 0.044 0.242 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.561 71.485 3376 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.15), residues: 3054 helix: 0.13 (0.15), residues: 1192 sheet: -2.13 (0.26), residues: 350 loop : -2.74 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 693 TYR 0.015 0.001 TYR A 668 PHE 0.019 0.001 PHE D 653 TRP 0.014 0.001 TRP D 610 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00252 (22668) covalent geometry : angle 0.61127 (31062) SS BOND : bond 0.00381 ( 18) SS BOND : angle 1.12191 ( 36) hydrogen bonds : bond 0.03391 ( 926) hydrogen bonds : angle 5.24575 ( 2664) Misc. bond : bond 0.00024 ( 2) link_BETA1-4 : bond 0.01129 ( 2) link_BETA1-4 : angle 3.37299 ( 6) link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 0.77246 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.8570 (m-30) cc_final: 0.8263 (t70) REVERT: A 491 MET cc_start: 0.8573 (mtp) cc_final: 0.8101 (mtm) REVERT: A 597 MET cc_start: 0.9103 (ttm) cc_final: 0.8404 (ttm) REVERT: B 59 PHE cc_start: 0.7744 (m-80) cc_final: 0.7321 (m-10) REVERT: B 463 ASP cc_start: 0.8667 (t70) cc_final: 0.8375 (t0) REVERT: B 561 MET cc_start: 0.8867 (ttm) cc_final: 0.8636 (ttm) REVERT: B 654 MET cc_start: 0.8457 (mtp) cc_final: 0.8243 (mtp) REVERT: B 829 MET cc_start: 0.9051 (mtp) cc_final: 0.8785 (mtp) REVERT: C 482 ASP cc_start: 0.8549 (m-30) cc_final: 0.8232 (t70) REVERT: D 561 MET cc_start: 0.8993 (ttm) cc_final: 0.8463 (ttm) REVERT: D 701 GLU cc_start: 0.8674 (mp0) cc_final: 0.8459 (pm20) REVERT: D 706 MET cc_start: 0.7300 (mpp) cc_final: 0.7048 (mtm) REVERT: D 809 MET cc_start: 0.8406 (tmm) cc_final: 0.8095 (tmm) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.0983 time to fit residues: 54.2991 Evaluate side-chains 246 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 203 optimal weight: 0.6980 chunk 240 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 153 GLN C 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.108568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090024 restraints weight = 87445.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.089562 restraints weight = 50146.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.090397 restraints weight = 45881.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.090996 restraints weight = 36034.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091119 restraints weight = 33067.412| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22694 Z= 0.139 Angle : 0.637 9.073 31116 Z= 0.330 Chirality : 0.045 0.232 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.425 71.667 3376 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.15), residues: 3054 helix: 0.14 (0.15), residues: 1192 sheet: -2.16 (0.26), residues: 362 loop : -2.64 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 693 TYR 0.020 0.001 TYR C 128 PHE 0.024 0.001 PHE D 653 TRP 0.022 0.002 TRP D 610 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00317 (22668) covalent geometry : angle 0.63414 (31062) SS BOND : bond 0.00385 ( 18) SS BOND : angle 1.27904 ( 36) hydrogen bonds : bond 0.03583 ( 926) hydrogen bonds : angle 5.26017 ( 2664) Misc. bond : bond 0.00044 ( 2) link_BETA1-4 : bond 0.00931 ( 2) link_BETA1-4 : angle 3.54116 ( 6) link_NAG-ASN : bond 0.00294 ( 4) link_NAG-ASN : angle 0.75116 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASP cc_start: 0.8583 (m-30) cc_final: 0.8334 (t70) REVERT: A 491 MET cc_start: 0.8543 (mtp) cc_final: 0.7762 (mtm) REVERT: A 493 PHE cc_start: 0.7950 (m-10) cc_final: 0.7649 (m-10) REVERT: A 522 MET cc_start: 0.7802 (ptm) cc_final: 0.7487 (ptt) REVERT: A 597 MET cc_start: 0.9164 (ttm) cc_final: 0.8377 (ttm) REVERT: B 59 PHE cc_start: 0.7753 (m-80) cc_final: 0.7316 (m-10) REVERT: B 561 MET cc_start: 0.8955 (ttm) cc_final: 0.8556 (ttm) REVERT: B 829 MET cc_start: 0.9040 (mtp) cc_final: 0.8814 (mtp) REVERT: C 375 MET cc_start: 0.8192 (tpt) cc_final: 0.7795 (tpp) REVERT: C 482 ASP cc_start: 0.8511 (m-30) cc_final: 0.8234 (t70) REVERT: C 597 MET cc_start: 0.9009 (ttt) cc_final: 0.8785 (ttm) REVERT: C 655 MET cc_start: 0.7956 (tpt) cc_final: 0.7661 (mmm) REVERT: C 723 MET cc_start: 0.5995 (mpp) cc_final: 0.5767 (mpp) REVERT: D 561 MET cc_start: 0.9071 (ttm) cc_final: 0.8660 (ttm) REVERT: D 809 MET cc_start: 0.8405 (tmm) cc_final: 0.8094 (tmm) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.0970 time to fit residues: 51.8554 Evaluate side-chains 235 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 107 optimal weight: 40.0000 chunk 231 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN A 498 HIS B 405 HIS C 426 GLN D 405 HIS D 703 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.109890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.091308 restraints weight = 89354.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.091124 restraints weight = 59158.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091642 restraints weight = 60919.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.092193 restraints weight = 43485.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092808 restraints weight = 39015.307| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22694 Z= 0.270 Angle : 0.789 13.053 31116 Z= 0.413 Chirality : 0.048 0.179 3796 Planarity : 0.005 0.041 3930 Dihedral : 8.130 82.813 3376 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.14), residues: 3054 helix: -0.38 (0.15), residues: 1180 sheet: -2.64 (0.25), residues: 346 loop : -2.75 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 380 TYR 0.026 0.002 TYR C 128 PHE 0.045 0.003 PHE D 653 TRP 0.042 0.003 TRP A 789 HIS 0.007 0.002 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00605 (22668) covalent geometry : angle 0.78619 (31062) SS BOND : bond 0.00471 ( 18) SS BOND : angle 1.48665 ( 36) hydrogen bonds : bond 0.04592 ( 926) hydrogen bonds : angle 5.78797 ( 2664) Misc. bond : bond 0.00091 ( 2) link_BETA1-4 : bond 0.00979 ( 2) link_BETA1-4 : angle 3.81789 ( 6) link_NAG-ASN : bond 0.00607 ( 4) link_NAG-ASN : angle 1.38579 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 MET cc_start: 0.9193 (ttm) cc_final: 0.8481 (ttm) REVERT: B 161 MET cc_start: 0.4830 (mtp) cc_final: 0.4335 (ttm) REVERT: B 285 TRP cc_start: 0.8088 (m100) cc_final: 0.7193 (m100) REVERT: B 478 LEU cc_start: 0.8416 (mt) cc_final: 0.7523 (mp) REVERT: B 552 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 561 MET cc_start: 0.8962 (ttm) cc_final: 0.8524 (ttm) REVERT: B 829 MET cc_start: 0.8879 (mtp) cc_final: 0.8592 (mtp) REVERT: C 597 MET cc_start: 0.9025 (ttt) cc_final: 0.8756 (ttm) REVERT: C 723 MET cc_start: 0.6380 (mpp) cc_final: 0.6150 (mpp) REVERT: D 478 LEU cc_start: 0.8180 (mt) cc_final: 0.7415 (mp) REVERT: D 702 MET cc_start: 0.8641 (mtt) cc_final: 0.7654 (mtm) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.0997 time to fit residues: 49.4964 Evaluate side-chains 226 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 206 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 303 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 171 optimal weight: 0.0170 chunk 238 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 225 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 426 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.116672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.098293 restraints weight = 88018.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.098027 restraints weight = 50472.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.098705 restraints weight = 41969.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.099253 restraints weight = 34219.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.099422 restraints weight = 30815.552| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22694 Z= 0.118 Angle : 0.647 11.079 31116 Z= 0.332 Chirality : 0.045 0.186 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.218 69.346 3376 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.15), residues: 3054 helix: 0.17 (0.15), residues: 1188 sheet: -2.12 (0.26), residues: 364 loop : -2.60 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 742 TYR 0.016 0.001 TYR C 128 PHE 0.032 0.002 PHE A 575 TRP 0.026 0.002 TRP D 285 HIS 0.009 0.001 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00252 (22668) covalent geometry : angle 0.64340 (31062) SS BOND : bond 0.01072 ( 18) SS BOND : angle 1.42358 ( 36) hydrogen bonds : bond 0.03641 ( 926) hydrogen bonds : angle 5.23138 ( 2664) Misc. bond : bond 0.00020 ( 2) link_BETA1-4 : bond 0.01046 ( 2) link_BETA1-4 : angle 3.59744 ( 6) link_NAG-ASN : bond 0.00338 ( 4) link_NAG-ASN : angle 0.58942 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8422 (tpt) cc_final: 0.8183 (tpt) REVERT: A 482 ASP cc_start: 0.8734 (m-30) cc_final: 0.8363 (t70) REVERT: A 522 MET cc_start: 0.8074 (ptm) cc_final: 0.7842 (ptt) REVERT: A 597 MET cc_start: 0.9165 (ttm) cc_final: 0.8458 (ttm) REVERT: A 598 LEU cc_start: 0.8969 (mt) cc_final: 0.8386 (mt) REVERT: A 655 MET cc_start: 0.7501 (mmp) cc_final: 0.6633 (mmm) REVERT: A 662 MET cc_start: 0.9030 (tmm) cc_final: 0.8764 (tmm) REVERT: A 759 PHE cc_start: 0.8287 (t80) cc_final: 0.8053 (t80) REVERT: B 59 PHE cc_start: 0.7258 (m-80) cc_final: 0.6963 (m-80) REVERT: B 161 MET cc_start: 0.4314 (mtp) cc_final: 0.3848 (ttm) REVERT: B 561 MET cc_start: 0.9007 (ttm) cc_final: 0.8576 (ttm) REVERT: B 829 MET cc_start: 0.8911 (mtp) cc_final: 0.8697 (mtp) REVERT: C 375 MET cc_start: 0.8066 (tpt) cc_final: 0.7665 (tpp) REVERT: C 376 ASN cc_start: 0.8706 (t0) cc_final: 0.8463 (t0) REVERT: C 482 ASP cc_start: 0.8669 (m-30) cc_final: 0.8328 (t70) REVERT: C 662 MET cc_start: 0.9109 (tmm) cc_final: 0.8829 (tmm) REVERT: D 561 MET cc_start: 0.9091 (ttm) cc_final: 0.8725 (ttm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1048 time to fit residues: 55.6814 Evaluate side-chains 231 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5415 > 50: distance: 19 - 23: 23.354 distance: 23 - 24: 36.596 distance: 24 - 25: 41.944 distance: 24 - 27: 18.838 distance: 25 - 26: 8.837 distance: 25 - 30: 29.242 distance: 27 - 28: 50.062 distance: 27 - 29: 42.165 distance: 30 - 31: 12.958 distance: 30 - 134: 13.622 distance: 31 - 32: 40.920 distance: 31 - 34: 29.777 distance: 32 - 33: 41.133 distance: 32 - 38: 36.184 distance: 33 - 131: 34.000 distance: 34 - 35: 42.408 distance: 34 - 36: 34.138 distance: 35 - 37: 40.520 distance: 38 - 39: 52.286 distance: 39 - 40: 45.714 distance: 39 - 42: 14.492 distance: 40 - 41: 39.136 distance: 40 - 45: 56.698 distance: 42 - 43: 37.969 distance: 42 - 44: 31.527 distance: 45 - 46: 47.557 distance: 45 - 122: 34.920 distance: 46 - 47: 47.224 distance: 46 - 49: 28.093 distance: 47 - 48: 39.023 distance: 47 - 54: 55.882 distance: 48 - 119: 35.444 distance: 49 - 50: 45.729 distance: 50 - 51: 18.879 distance: 51 - 53: 40.183 distance: 54 - 55: 40.223 distance: 55 - 56: 37.036 distance: 55 - 58: 40.235 distance: 56 - 57: 30.548 distance: 56 - 60: 22.047 distance: 58 - 59: 56.395 distance: 60 - 61: 58.388 distance: 61 - 62: 57.535 distance: 61 - 64: 51.779 distance: 62 - 63: 56.696 distance: 64 - 65: 9.758 distance: 64 - 66: 16.162 distance: 67 - 68: 38.569 distance: 68 - 69: 53.114 distance: 68 - 71: 42.181 distance: 69 - 70: 30.987 distance: 69 - 75: 50.708 distance: 71 - 72: 49.371 distance: 72 - 73: 20.005 distance: 72 - 74: 16.538 distance: 75 - 76: 28.769 distance: 75 - 81: 38.457 distance: 76 - 77: 38.092 distance: 76 - 79: 23.449 distance: 77 - 78: 14.433 distance: 77 - 82: 44.074 distance: 79 - 80: 18.790 distance: 80 - 81: 23.199 distance: 82 - 83: 23.453 distance: 83 - 84: 42.828 distance: 83 - 86: 25.969 distance: 84 - 85: 41.006 distance: 84 - 87: 55.722 distance: 87 - 88: 47.442 distance: 88 - 89: 35.214 distance: 88 - 91: 23.701 distance: 89 - 93: 20.727 distance: 91 - 92: 19.203