Starting phenix.real_space_refine on Sun Jun 29 08:11:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9a_36982/06_2025/8k9a_36982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9a_36982/06_2025/8k9a_36982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9a_36982/06_2025/8k9a_36982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9a_36982/06_2025/8k9a_36982.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9a_36982/06_2025/8k9a_36982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9a_36982/06_2025/8k9a_36982.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 22033 2.51 5 N 5506 2.21 5 O 6366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 1.78s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 8081 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 950} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 8057 Classifications: {'peptide': 969} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 949} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 8091 Classifications: {'peptide': 971} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 950} Chain breaks: 3 Chain: "D" Number of atoms: 8093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8093 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 20.66, per 1000 atoms: 0.61 Number of scatterers: 34035 At special positions: 0 Unit cell: (102, 130.05, 275.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 6366 8.00 N 5506 7.00 C 22033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.93 Conformation dependent library (CDL) restraints added in 3.9 seconds 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7830 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 16 sheets defined 65.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.447A pdb=" N GLU A 13 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.580A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.659A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.543A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.710A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.548A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.991A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.610A pdb=" N ILE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.632A pdb=" N TYR A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.703A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.723A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.934A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.661A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 467 through 493 removed outlier: 3.856A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.357A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.623A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.772A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 702 removed outlier: 3.653A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 702 " --> pdb=" O GLN A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.956A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.623A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.729A pdb=" N LYS A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.804A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.745A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.654A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.749A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 872 removed outlier: 3.693A pdb=" N ILE A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 896 Processing helix chain 'A' and resid 913 through 922 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.685A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.575A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.025A pdb=" N TRP A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 977 through 991 Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.958A pdb=" N ILE A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.776A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.890A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.506A pdb=" N ALA B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.667A pdb=" N ASN B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.814A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 282 through 299 removed outlier: 3.567A pdb=" N TYR B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.513A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.558A pdb=" N LEU B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.913A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 468 through 492 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.796A pdb=" N ALA B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.656A pdb=" N MET B 531 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.792A pdb=" N TYR B 552 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.973A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.116A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.897A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.565A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.421A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.279A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.584A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.783A pdb=" N GLU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.600A pdb=" N LEU B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.937A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 872 removed outlier: 3.523A pdb=" N MET B 866 " --> pdb=" O ILE B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 896 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.694A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 4.257A pdb=" N TRP B 958 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 991 removed outlier: 4.241A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.772A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.650A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.638A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.792A pdb=" N CYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.045A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.848A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.605A pdb=" N SER C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.580A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 417 through 427 removed outlier: 4.002A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 468 through 496 Processing helix chain 'C' and resid 508 through 520 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.734A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 571 removed outlier: 3.723A pdb=" N TYR C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C 557 " --> pdb=" O ASP C 553 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 571 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.766A pdb=" N ASN C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.626A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 648 through 658 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 removed outlier: 3.500A pdb=" N LYS C 675 " --> pdb=" O SER C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 701 removed outlier: 3.743A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 removed outlier: 4.040A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.579A pdb=" N LYS C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.580A pdb=" N ILE C 772 " --> pdb=" O PRO C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 removed outlier: 4.020A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.764A pdb=" N CYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 840 removed outlier: 3.633A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 845 Processing helix chain 'C' and resid 846 through 854 Processing helix chain 'C' and resid 862 through 872 removed outlier: 3.739A pdb=" N ASN C 867 " --> pdb=" O ASN C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 896 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 929 through 933 removed outlier: 3.981A pdb=" N PHE C 933 " --> pdb=" O MET C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 removed outlier: 3.700A pdb=" N ASP C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.704A pdb=" N LYS C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 962 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 976 through 991 removed outlier: 4.712A pdb=" N GLU C 982 " --> pdb=" O HIS C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1003 Processing helix chain 'D' and resid 9 through 20 removed outlier: 3.979A pdb=" N GLU D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.639A pdb=" N THR D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 53' Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.641A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.854A pdb=" N TYR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 108 removed outlier: 3.531A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.718A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.644A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.824A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.502A pdb=" N GLU D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.943A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.857A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 468 through 493 removed outlier: 3.842A pdb=" N ASN D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 removed outlier: 3.786A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.494A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.639A pdb=" N ASN D 563 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.679A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.770A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.599A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 681 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.765A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'D' and resid 768 through 785 removed outlier: 3.513A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.922A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 3.651A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.535A pdb=" N ILE D 835 " --> pdb=" O LYS D 831 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 855 removed outlier: 3.534A pdb=" N SER D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 871 removed outlier: 4.067A pdb=" N MET D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 896 Processing helix chain 'D' and resid 912 through 922 removed outlier: 3.596A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 934 removed outlier: 3.825A pdb=" N GLU D 931 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 955 through 961 removed outlier: 3.506A pdb=" N TRP D 958 " --> pdb=" O ILE D 955 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 960 " --> pdb=" O SER D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 977 through 991 Processing helix chain 'D' and resid 993 through 1003 Processing helix chain 'E' and resid 95 through 104 Processing helix chain 'F' and resid 10 through 13 removed outlier: 3.554A pdb=" N ASP F 13 " --> pdb=" O ALA F 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 95 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.281A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 341 removed outlier: 3.675A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.306A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 246 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.171A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 42 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 246 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA8, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.348A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.938A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.279A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 71 through 72 removed outlier: 8.831A pdb=" N VAL E 117 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS E 46 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.169A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.169A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU F 115 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 46 " --> pdb=" O GLU F 115 " (cutoff:3.500A) 1726 hydrogen bonds defined for protein. 4977 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: 14.14 Time building geometry restraints manager: 9.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10786 1.34 - 1.46: 8697 1.46 - 1.58: 15115 1.58 - 1.70: 0 1.70 - 1.82: 214 Bond restraints: 34812 Sorted by residual: bond pdb=" N VAL C 859 " pdb=" CA VAL C 859 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" C VAL C 859 " pdb=" N GLU C 860 " ideal model delta sigma weight residual 1.331 1.289 0.041 1.31e-02 5.83e+03 1.00e+01 bond pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 1.462 1.495 -0.032 1.06e-02 8.90e+03 9.27e+00 bond pdb=" N VAL E 99 " pdb=" CA VAL E 99 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.74e+00 bond pdb=" N ILE B 138 " pdb=" CA ILE B 138 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.41e-02 5.03e+03 8.01e+00 ... (remaining 34807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 46269 2.35 - 4.70: 519 4.70 - 7.06: 79 7.06 - 9.41: 23 9.41 - 11.76: 9 Bond angle restraints: 46899 Sorted by residual: angle pdb=" N THR E 11 " pdb=" CA THR E 11 " pdb=" C THR E 11 " ideal model delta sigma weight residual 113.37 107.26 6.11 1.38e+00 5.25e-01 1.96e+01 angle pdb=" N TYR C 650 " pdb=" CA TYR C 650 " pdb=" C TYR C 650 " ideal model delta sigma weight residual 111.71 106.66 5.05 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N ILE C 138 " pdb=" CA ILE C 138 " pdb=" C ILE C 138 " ideal model delta sigma weight residual 112.98 107.76 5.22 1.25e+00 6.40e-01 1.75e+01 angle pdb=" N THR C 555 " pdb=" CA THR C 555 " pdb=" C THR C 555 " ideal model delta sigma weight residual 112.90 107.59 5.31 1.31e+00 5.83e-01 1.64e+01 angle pdb=" CA THR C 555 " pdb=" CB THR C 555 " pdb=" OG1 THR C 555 " ideal model delta sigma weight residual 109.60 103.56 6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 46894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17358 17.86 - 35.72: 2530 35.72 - 53.59: 683 53.59 - 71.45: 125 71.45 - 89.31: 41 Dihedral angle restraints: 20737 sinusoidal: 8568 harmonic: 12169 Sorted by residual: dihedral pdb=" CA MET C 647 " pdb=" C MET C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASN B 705 " pdb=" C ASN B 705 " pdb=" N VAL B 706 " pdb=" CA VAL B 706 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LYS B 505 " pdb=" C LYS B 505 " pdb=" N PRO B 506 " pdb=" CA PRO B 506 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 20734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4171 0.055 - 0.110: 736 0.110 - 0.164: 83 0.164 - 0.219: 10 0.219 - 0.274: 3 Chirality restraints: 5003 Sorted by residual: chirality pdb=" CG LEU D 922 " pdb=" CB LEU D 922 " pdb=" CD1 LEU D 922 " pdb=" CD2 LEU D 922 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 859 " pdb=" CA VAL C 859 " pdb=" CG1 VAL C 859 " pdb=" CG2 VAL C 859 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE C 661 " pdb=" CA ILE C 661 " pdb=" CG1 ILE C 661 " pdb=" CG2 ILE C 661 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 5000 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 462 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C SER B 462 " 0.049 2.00e-02 2.50e+03 pdb=" O SER B 462 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 463 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 660 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C LYS D 660 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS D 660 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE D 661 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 458 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ILE B 458 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 458 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 459 " 0.015 2.00e-02 2.50e+03 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 397 2.63 - 3.19: 31273 3.19 - 3.76: 52758 3.76 - 4.33: 68558 4.33 - 4.90: 112387 Nonbonded interactions: 265373 Sorted by model distance: nonbonded pdb=" OH TYR C 687 " pdb=" OE2 GLU C 715 " model vdw 2.057 3.040 nonbonded pdb=" O GLU C 516 " pdb=" OG1 THR C 520 " model vdw 2.127 3.040 nonbonded pdb=" O ILE C 458 " pdb=" OG SER C 462 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.138 3.040 nonbonded pdb=" OD1 ASP C 630 " pdb=" OG SER D 991 " model vdw 2.147 3.040 ... (remaining 265368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 142 or resid 145 through 463 or resid 465 throu \ gh 498 or resid 503 through 747 or resid 749 through 753 or (resid 754 and (name \ N or name CA or name C or name O or name CB )) or resid 755 through 787 or resi \ d 794 through 896 or resid 910 through 1005)) selection = (chain 'B' and (resid 22 through 463 or resid 465 through 566 or resid 578 throu \ gh 747 or resid 749 through 759 or (resid 760 and (name N or name CA or name C o \ r name O or name CB )) or resid 761 through 787 or resid 794 through 857 or resi \ d 861 through 896 or resid 910 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 974 or resid 976 through \ 1005)) selection = (chain 'C' and (resid 22 through 142 or resid 145 through 463 or resid 465 throu \ gh 498 or resid 503 through 504 or (resid 505 and (name N or name CA or name C o \ r name O or name CB )) or resid 506 through 566 or resid 578 through 753 or (res \ id 754 and (name N or name CA or name C or name O or name CB )) or resid 755 thr \ ough 759 or (resid 760 and (name N or name CA or name C or name O or name CB )) \ or resid 761 through 787 or resid 794 through 857 or resid 861 through 896 or re \ sid 910 through 911 or (resid 912 and (name N or name CA or name C or name O or \ name CB )) or resid 913 through 974 or resid 976 through 1005)) selection = (chain 'D' and (resid 22 through 142 or resid 145 through 498 or resid 503 throu \ gh 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 747 or resid 749 through 753 or (resid 754 and (name N or nam \ e CA or name C or name O or name CB )) or resid 755 through 759 or (resid 760 an \ d (name N or name CA or name C or name O or name CB )) or resid 761 through 787 \ or resid 794 through 857 or resid 861 through 896 or resid 910 through 1005)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 10 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 120)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.320 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 74.450 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34812 Z= 0.165 Angle : 0.639 11.761 46899 Z= 0.344 Chirality : 0.042 0.274 5003 Planarity : 0.004 0.059 5976 Dihedral : 17.913 89.311 12907 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 2.33 % Allowed : 29.78 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 4060 helix: 0.97 (0.11), residues: 2380 sheet: -1.59 (0.35), residues: 214 loop : -1.17 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 757 HIS 0.005 0.001 HIS C 979 PHE 0.038 0.001 PHE C 778 TYR 0.037 0.001 TYR D 888 ARG 0.013 0.000 ARG A 669 Details of bonding type rmsd hydrogen bonds : bond 0.14562 ( 1724) hydrogen bonds : angle 5.61292 ( 4977) covalent geometry : bond 0.00303 (34812) covalent geometry : angle 0.63924 (46899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 246 time to evaluate : 3.890 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 811 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7738 (t80) REVERT: B 647 MET cc_start: 0.8087 (pmm) cc_final: 0.7751 (pmm) REVERT: C 651 ASP cc_start: 0.8686 (t70) cc_final: 0.8413 (t0) REVERT: C 751 ILE cc_start: 0.8529 (mp) cc_final: 0.8205 (tp) REVERT: D 519 MET cc_start: 0.8287 (mtm) cc_final: 0.7929 (mpp) outliers start: 87 outliers final: 68 residues processed: 316 average time/residue: 0.4051 time to fit residues: 218.5734 Evaluate side-chains 291 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 757 TRP Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 828 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 1004 PHE Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 371 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 297 GLN B 339 HIS B 382 ASN B 391 ASN B 415 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 867 ASN C 58 GLN C 115 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS ** C 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 ASN C 895 ASN D 224 ASN D 477 ASN D 789 GLN D 832 GLN F 54 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.107007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068385 restraints weight = 92445.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069412 restraints weight = 64634.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069995 restraints weight = 47033.102| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34812 Z= 0.118 Angle : 0.543 10.144 46899 Z= 0.280 Chirality : 0.039 0.173 5003 Planarity : 0.003 0.053 5976 Dihedral : 5.903 58.128 4613 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 3.42 % Allowed : 26.81 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4060 helix: 1.27 (0.11), residues: 2411 sheet: -1.63 (0.35), residues: 200 loop : -1.08 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 143 HIS 0.004 0.001 HIS D 503 PHE 0.015 0.001 PHE D 839 TYR 0.028 0.001 TYR D 888 ARG 0.005 0.000 ARG D 669 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1724) hydrogen bonds : angle 4.17944 ( 4977) covalent geometry : bond 0.00263 (34812) covalent geometry : angle 0.54342 (46899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 254 time to evaluate : 4.307 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 421 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8775 (mtm) REVERT: A 744 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 115 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: B 342 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8614 (t) REVERT: B 517 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7139 (ttp80) REVERT: B 647 MET cc_start: 0.8637 (pmm) cc_final: 0.8344 (pmm) REVERT: B 838 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5748 (mm) REVERT: B 936 MET cc_start: 0.3393 (OUTLIER) cc_final: 0.3108 (mmt) REVERT: C 124 MET cc_start: 0.8976 (mmm) cc_final: 0.8670 (mmm) REVERT: C 396 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8061 (mmt) REVERT: C 599 CYS cc_start: 0.7444 (t) cc_final: 0.7052 (t) REVERT: C 741 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9054 (mm) REVERT: C 913 MET cc_start: 0.7072 (ppp) cc_final: 0.6744 (ttt) REVERT: C 993 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8762 (t0) REVERT: D 825 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7533 (mm) REVERT: E 85 LYS cc_start: 0.8637 (mptt) cc_final: 0.8435 (mptt) REVERT: F 47 CYS cc_start: 0.7836 (t) cc_final: 0.7393 (t) outliers start: 128 outliers final: 53 residues processed: 351 average time/residue: 0.4318 time to fit residues: 256.8427 Evaluate side-chains 292 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 229 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 366 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 349 optimal weight: 1.9990 chunk 406 optimal weight: 9.9990 chunk 83 optimal weight: 0.0170 chunk 283 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 217 optimal weight: 0.3980 chunk 379 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN D 224 ASN E 17 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067894 restraints weight = 93874.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.068497 restraints weight = 66221.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.068577 restraints weight = 48074.786| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34812 Z= 0.142 Angle : 0.527 8.478 46899 Z= 0.274 Chirality : 0.040 0.226 5003 Planarity : 0.003 0.049 5976 Dihedral : 4.961 56.872 4538 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer: Outliers : 3.39 % Allowed : 26.68 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 4060 helix: 1.34 (0.11), residues: 2410 sheet: -1.42 (0.38), residues: 178 loop : -1.08 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 919 HIS 0.004 0.001 HIS B 67 PHE 0.038 0.001 PHE A 839 TYR 0.021 0.001 TYR D 888 ARG 0.003 0.000 ARG D 760 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1724) hydrogen bonds : angle 4.03426 ( 4977) covalent geometry : bond 0.00323 (34812) covalent geometry : angle 0.52663 (46899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 255 time to evaluate : 4.109 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 9 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8683 (tptp) REVERT: A 711 GLN cc_start: 0.9165 (tt0) cc_final: 0.8525 (tm-30) REVERT: A 744 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8332 (t80) REVERT: B 342 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (t) REVERT: B 368 ASP cc_start: 0.8985 (m-30) cc_final: 0.8337 (t0) REVERT: B 647 MET cc_start: 0.8504 (pmm) cc_final: 0.8277 (pmm) REVERT: B 838 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5750 (mm) REVERT: B 921 PHE cc_start: 0.3641 (t80) cc_final: 0.3434 (t80) REVERT: B 936 MET cc_start: 0.3374 (OUTLIER) cc_final: 0.3112 (mmt) REVERT: C 124 MET cc_start: 0.9016 (mmm) cc_final: 0.8722 (mmm) REVERT: C 134 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7688 (p90) REVERT: C 279 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: C 396 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8098 (mmt) REVERT: D 223 TYR cc_start: 0.7953 (t80) cc_final: 0.7705 (t80) REVERT: D 230 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8611 (t0) REVERT: D 432 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 825 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7565 (mm) REVERT: D 930 MET cc_start: 0.8195 (pmm) cc_final: 0.7910 (pmm) REVERT: D 936 MET cc_start: 0.3716 (mtt) cc_final: 0.3397 (mtt) REVERT: E 67 PHE cc_start: 0.7794 (m-80) cc_final: 0.7262 (m-80) REVERT: E 110 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6795 (m-80) outliers start: 127 outliers final: 63 residues processed: 352 average time/residue: 0.4262 time to fit residues: 253.9330 Evaluate side-chains 298 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 356 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 350 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 HIS C 895 ASN D 224 ASN ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.067948 restraints weight = 93829.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068078 restraints weight = 64487.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067763 restraints weight = 51536.859| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34812 Z= 0.150 Angle : 0.535 11.600 46899 Z= 0.277 Chirality : 0.040 0.198 5003 Planarity : 0.003 0.049 5976 Dihedral : 4.835 59.190 4532 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 3.66 % Allowed : 26.97 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 4060 helix: 1.36 (0.11), residues: 2428 sheet: -1.50 (0.36), residues: 200 loop : -1.08 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 143 HIS 0.005 0.001 HIS F 88 PHE 0.022 0.001 PHE D 839 TYR 0.028 0.001 TYR D 888 ARG 0.007 0.000 ARG C 502 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1724) hydrogen bonds : angle 3.98008 ( 4977) covalent geometry : bond 0.00350 (34812) covalent geometry : angle 0.53483 (46899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 243 time to evaluate : 4.245 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 9 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8687 (tptp) REVERT: A 421 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8738 (mtm) REVERT: A 711 GLN cc_start: 0.9197 (tt0) cc_final: 0.8607 (tm-30) REVERT: A 744 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8452 (t80) REVERT: A 802 ARG cc_start: 0.8292 (ptt90) cc_final: 0.7893 (tmt-80) REVERT: A 936 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.2742 (ptp) REVERT: B 342 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8598 (t) REVERT: B 460 LEU cc_start: 0.9294 (pp) cc_final: 0.8907 (mm) REVERT: B 517 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7176 (ttp80) REVERT: B 648 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: B 838 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5773 (mm) REVERT: B 921 PHE cc_start: 0.3647 (t80) cc_final: 0.3399 (t80) REVERT: B 936 MET cc_start: 0.3260 (OUTLIER) cc_final: 0.3030 (mmt) REVERT: B 954 PHE cc_start: 0.5212 (t80) cc_final: 0.4920 (t80) REVERT: C 124 MET cc_start: 0.9048 (mmm) cc_final: 0.8724 (mmm) REVERT: C 134 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.7773 (p90) REVERT: C 279 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: C 359 ARG cc_start: 0.8667 (tpt170) cc_final: 0.8422 (tpt-90) REVERT: C 396 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7905 (mmm) REVERT: C 751 ILE cc_start: 0.8580 (mp) cc_final: 0.8216 (tp) REVERT: C 825 LEU cc_start: 0.5728 (mt) cc_final: 0.5434 (mt) REVERT: D 223 TYR cc_start: 0.7954 (t80) cc_final: 0.7731 (t80) REVERT: D 230 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8325 (t0) REVERT: D 396 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6963 (mmt) REVERT: D 825 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7624 (mm) REVERT: D 930 MET cc_start: 0.8130 (pmm) cc_final: 0.7812 (pmm) REVERT: D 936 MET cc_start: 0.3827 (mtt) cc_final: 0.3537 (mtt) REVERT: E 16 TYR cc_start: 0.7092 (t80) cc_final: 0.6750 (t80) REVERT: E 67 PHE cc_start: 0.7747 (m-80) cc_final: 0.7359 (m-80) REVERT: E 110 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6887 (m-80) outliers start: 137 outliers final: 79 residues processed: 349 average time/residue: 0.4259 time to fit residues: 252.3111 Evaluate side-chains 322 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 229 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 757 TRP Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 115 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 396 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 HIS B 782 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN C 606 HIS D 109 GLN D 224 ASN ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.066440 restraints weight = 93673.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.066660 restraints weight = 63494.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066926 restraints weight = 50181.508| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34812 Z= 0.183 Angle : 0.553 11.159 46899 Z= 0.288 Chirality : 0.040 0.185 5003 Planarity : 0.003 0.053 5976 Dihedral : 4.913 58.082 4532 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 4.06 % Allowed : 26.78 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 4060 helix: 1.33 (0.11), residues: 2429 sheet: -1.49 (0.36), residues: 190 loop : -1.12 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 958 HIS 0.005 0.001 HIS B 67 PHE 0.021 0.001 PHE D 839 TYR 0.021 0.001 TYR D 888 ARG 0.005 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 1724) hydrogen bonds : angle 4.03435 ( 4977) covalent geometry : bond 0.00431 (34812) covalent geometry : angle 0.55332 (46899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 245 time to evaluate : 4.448 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 9 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8721 (tptp) REVERT: A 421 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8738 (mtm) REVERT: A 711 GLN cc_start: 0.9211 (tt0) cc_final: 0.8593 (tm-30) REVERT: A 744 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8432 (t80) REVERT: A 802 ARG cc_start: 0.8268 (ptt90) cc_final: 0.7857 (tmt-80) REVERT: A 936 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.2782 (ptp) REVERT: B 115 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: B 283 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9006 (tt) REVERT: B 342 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8644 (t) REVERT: B 460 LEU cc_start: 0.9247 (pp) cc_final: 0.8854 (mm) REVERT: B 782 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: B 835 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6616 (mp) REVERT: B 838 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5842 (mm) REVERT: B 921 PHE cc_start: 0.3507 (t80) cc_final: 0.3236 (t80) REVERT: B 936 MET cc_start: 0.3177 (OUTLIER) cc_final: 0.2945 (mmt) REVERT: B 954 PHE cc_start: 0.5272 (t80) cc_final: 0.4989 (t80) REVERT: C 124 MET cc_start: 0.9066 (mmm) cc_final: 0.8733 (mmm) REVERT: C 134 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7818 (p90) REVERT: C 359 ARG cc_start: 0.8650 (tpt170) cc_final: 0.8262 (tpp-160) REVERT: C 396 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: C 421 MET cc_start: 0.8787 (pmt) cc_final: 0.8158 (pmt) REVERT: C 588 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9021 (tp) REVERT: C 599 CYS cc_start: 0.7535 (t) cc_final: 0.7219 (t) REVERT: C 738 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8734 (tptt) REVERT: C 751 ILE cc_start: 0.8664 (mp) cc_final: 0.8463 (tp) REVERT: C 825 LEU cc_start: 0.5807 (mt) cc_final: 0.5492 (mt) REVERT: C 1005 ILE cc_start: 0.8189 (mm) cc_final: 0.7579 (pt) REVERT: D 188 ASP cc_start: 0.8648 (t0) cc_final: 0.8250 (t0) REVERT: D 230 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8362 (t0) REVERT: D 825 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7677 (mm) REVERT: D 930 MET cc_start: 0.8093 (pmm) cc_final: 0.7537 (pmm) REVERT: D 936 MET cc_start: 0.3713 (mtt) cc_final: 0.3458 (mtt) REVERT: E 16 TYR cc_start: 0.7061 (t80) cc_final: 0.6710 (t80) REVERT: E 47 CYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6021 (t) REVERT: E 67 PHE cc_start: 0.7711 (m-80) cc_final: 0.7340 (m-80) REVERT: E 110 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: F 51 TYR cc_start: 0.8616 (m-10) cc_final: 0.8332 (m-10) outliers start: 152 outliers final: 87 residues processed: 367 average time/residue: 0.4530 time to fit residues: 280.7271 Evaluate side-chains 328 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 223 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 782 GLN Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 504 TYR Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 757 TRP Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 736 ILE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 353 optimal weight: 0.6980 chunk 287 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 367 optimal weight: 0.0470 chunk 247 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 990 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 GLN D 224 ASN ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067181 restraints weight = 93011.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068725 restraints weight = 62295.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068906 restraints weight = 47636.022| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34812 Z= 0.102 Angle : 0.518 11.077 46899 Z= 0.267 Chirality : 0.039 0.266 5003 Planarity : 0.003 0.052 5976 Dihedral : 4.618 56.070 4526 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 3.42 % Allowed : 27.24 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 4060 helix: 1.44 (0.11), residues: 2423 sheet: -1.36 (0.37), residues: 176 loop : -1.05 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 143 HIS 0.003 0.001 HIS B 128 PHE 0.022 0.001 PHE D 839 TYR 0.023 0.001 TYR D 888 ARG 0.004 0.000 ARG D 819 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 1724) hydrogen bonds : angle 3.85242 ( 4977) covalent geometry : bond 0.00224 (34812) covalent geometry : angle 0.51773 (46899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 254 time to evaluate : 3.824 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 9 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8721 (tptp) REVERT: A 711 GLN cc_start: 0.9183 (tt0) cc_final: 0.8553 (tm-30) REVERT: A 744 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8525 (t80) REVERT: A 802 ARG cc_start: 0.8313 (ptt90) cc_final: 0.7829 (ttt180) REVERT: A 913 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6018 (pp-130) REVERT: A 936 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.2916 (ptp) REVERT: A 939 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8451 (pp30) REVERT: A 1004 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 283 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8934 (tt) REVERT: B 342 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8649 (t) REVERT: B 460 LEU cc_start: 0.9217 (pp) cc_final: 0.8823 (mm) REVERT: B 467 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7271 (p0) REVERT: B 517 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7240 (ttp80) REVERT: B 648 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: B 835 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6687 (mp) REVERT: B 838 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5844 (mm) REVERT: B 921 PHE cc_start: 0.3543 (t80) cc_final: 0.3237 (t80) REVERT: B 954 PHE cc_start: 0.5246 (t80) cc_final: 0.4952 (t80) REVERT: C 124 MET cc_start: 0.9035 (mmm) cc_final: 0.8716 (mmm) REVERT: C 134 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7735 (p90) REVERT: C 359 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8220 (tpp-160) REVERT: C 396 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7868 (mmm) REVERT: C 421 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.7801 (pmm) REVERT: C 588 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8990 (tp) REVERT: C 599 CYS cc_start: 0.7502 (t) cc_final: 0.7151 (t) REVERT: C 738 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8744 (tptt) REVERT: C 749 LEU cc_start: 0.7041 (mp) cc_final: 0.6739 (tp) REVERT: C 825 LEU cc_start: 0.5834 (mt) cc_final: 0.5510 (mt) REVERT: C 892 ARG cc_start: 0.8146 (mmp-170) cc_final: 0.7388 (ptp-170) REVERT: C 1005 ILE cc_start: 0.8118 (mm) cc_final: 0.7454 (pt) REVERT: D 147 LYS cc_start: 0.5464 (tptp) cc_final: 0.4525 (mptt) REVERT: D 188 ASP cc_start: 0.8574 (t0) cc_final: 0.8023 (t0) REVERT: D 223 TYR cc_start: 0.7882 (t80) cc_final: 0.7600 (t80) REVERT: D 230 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8430 (t0) REVERT: D 616 MET cc_start: 0.9231 (tpp) cc_final: 0.9017 (mmt) REVERT: D 729 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7728 (p) REVERT: D 825 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 930 MET cc_start: 0.8064 (pmm) cc_final: 0.7463 (pmm) REVERT: D 936 MET cc_start: 0.3661 (mtt) cc_final: 0.3403 (mtt) REVERT: E 16 TYR cc_start: 0.6995 (t80) cc_final: 0.6610 (t80) REVERT: E 47 CYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5884 (t) REVERT: E 67 PHE cc_start: 0.7753 (m-80) cc_final: 0.7409 (m-80) REVERT: E 110 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: F 51 TYR cc_start: 0.8615 (m-10) cc_final: 0.8346 (m-10) REVERT: F 71 LYS cc_start: 0.8729 (tptt) cc_final: 0.8479 (tptt) outliers start: 128 outliers final: 70 residues processed: 354 average time/residue: 0.4261 time to fit residues: 253.1600 Evaluate side-chains 324 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 233 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 92 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN D 786 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.104390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066426 restraints weight = 93955.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067148 restraints weight = 63838.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066962 restraints weight = 47622.226| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34812 Z= 0.167 Angle : 0.561 14.567 46899 Z= 0.288 Chirality : 0.040 0.264 5003 Planarity : 0.003 0.053 5976 Dihedral : 4.697 58.634 4526 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 3.29 % Allowed : 27.72 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 4060 helix: 1.32 (0.11), residues: 2433 sheet: -1.48 (0.37), residues: 176 loop : -1.10 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 919 HIS 0.005 0.001 HIS B 67 PHE 0.021 0.001 PHE D 839 TYR 0.025 0.001 TYR D 888 ARG 0.004 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1724) hydrogen bonds : angle 3.96406 ( 4977) covalent geometry : bond 0.00392 (34812) covalent geometry : angle 0.56123 (46899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 234 time to evaluate : 4.350 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 9 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8712 (tptp) REVERT: A 421 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8690 (mtm) REVERT: A 678 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 744 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 802 ARG cc_start: 0.8283 (ptt90) cc_final: 0.7814 (ttt180) REVERT: A 936 MET cc_start: 0.3869 (OUTLIER) cc_final: 0.1867 (ptm) REVERT: A 939 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8451 (pp30) REVERT: A 1004 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6952 (t80) REVERT: B 283 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8978 (tt) REVERT: B 342 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8648 (t) REVERT: B 421 MET cc_start: 0.7768 (pmm) cc_final: 0.7379 (pmm) REVERT: B 517 ARG cc_start: 0.7917 (ptt-90) cc_final: 0.7244 (ttp80) REVERT: B 648 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: B 835 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6665 (mp) REVERT: B 838 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5854 (mm) REVERT: B 919 TRP cc_start: 0.6557 (m-10) cc_final: 0.6069 (m-90) REVERT: B 921 PHE cc_start: 0.3593 (t80) cc_final: 0.3287 (t80) REVERT: C 124 MET cc_start: 0.9072 (mmm) cc_final: 0.8757 (mmm) REVERT: C 134 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7785 (p90) REVERT: C 359 ARG cc_start: 0.8716 (tpt170) cc_final: 0.8365 (tpp-160) REVERT: C 396 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7956 (mmm) REVERT: C 421 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8392 (pmt) REVERT: C 588 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8888 (tp) REVERT: C 599 CYS cc_start: 0.7562 (t) cc_final: 0.7233 (t) REVERT: C 738 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8748 (tptt) REVERT: C 825 LEU cc_start: 0.5821 (mt) cc_final: 0.5472 (mt) REVERT: C 892 ARG cc_start: 0.8155 (mmp-170) cc_final: 0.7501 (ptp-170) REVERT: D 147 LYS cc_start: 0.5747 (tptp) cc_final: 0.4679 (mptt) REVERT: D 188 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8186 (t0) REVERT: D 223 TYR cc_start: 0.8001 (t80) cc_final: 0.7720 (t80) REVERT: D 230 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8431 (t0) REVERT: D 825 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7688 (mm) REVERT: D 930 MET cc_start: 0.8035 (pmm) cc_final: 0.7336 (pmm) REVERT: E 16 TYR cc_start: 0.7055 (t80) cc_final: 0.6649 (t80) REVERT: E 47 CYS cc_start: 0.6698 (OUTLIER) cc_final: 0.5931 (t) REVERT: E 67 PHE cc_start: 0.7705 (m-80) cc_final: 0.7341 (m-80) REVERT: E 110 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: F 51 TYR cc_start: 0.8645 (m-10) cc_final: 0.8317 (m-10) REVERT: F 71 LYS cc_start: 0.8712 (tptt) cc_final: 0.8471 (tptt) outliers start: 123 outliers final: 81 residues processed: 335 average time/residue: 0.4246 time to fit residues: 241.3862 Evaluate side-chains 322 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 220 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 648 GLU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 chunk 276 optimal weight: 0.0870 chunk 314 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 300 optimal weight: 0.5980 chunk 198 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 236 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS D 224 ASN D 786 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068440 restraints weight = 92368.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.068795 restraints weight = 62100.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.068783 restraints weight = 47970.412| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34812 Z= 0.100 Angle : 0.529 11.539 46899 Z= 0.270 Chirality : 0.039 0.236 5003 Planarity : 0.003 0.052 5976 Dihedral : 4.593 57.961 4526 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 2.70 % Allowed : 28.01 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 4060 helix: 1.42 (0.11), residues: 2423 sheet: -1.36 (0.37), residues: 176 loop : -1.05 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 919 HIS 0.022 0.001 HIS D 786 PHE 0.022 0.001 PHE F 59 TYR 0.026 0.001 TYR D 888 ARG 0.004 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 1724) hydrogen bonds : angle 3.80378 ( 4977) covalent geometry : bond 0.00219 (34812) covalent geometry : angle 0.52904 (46899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 246 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8718 (tptp) REVERT: A 421 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8643 (mtm) REVERT: A 678 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7883 (t80) REVERT: A 744 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8591 (t80) REVERT: A 802 ARG cc_start: 0.8263 (ptt90) cc_final: 0.7793 (ttt180) REVERT: A 913 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5634 (pp-130) REVERT: A 936 MET cc_start: 0.3795 (OUTLIER) cc_final: 0.1836 (ptm) REVERT: A 939 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: A 1004 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6932 (t80) REVERT: B 283 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8910 (tt) REVERT: B 342 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8632 (t) REVERT: B 421 MET cc_start: 0.7781 (pmm) cc_final: 0.7386 (pmm) REVERT: B 517 ARG cc_start: 0.7904 (ptt-90) cc_final: 0.7186 (ttp80) REVERT: B 648 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: B 835 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6679 (mp) REVERT: B 838 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5854 (mm) REVERT: B 919 TRP cc_start: 0.6415 (m-10) cc_final: 0.6191 (m-90) REVERT: B 921 PHE cc_start: 0.3475 (t80) cc_final: 0.3159 (t80) REVERT: C 124 MET cc_start: 0.9025 (mmm) cc_final: 0.8728 (mmm) REVERT: C 134 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7659 (p90) REVERT: C 359 ARG cc_start: 0.8694 (tpt170) cc_final: 0.8299 (tpp-160) REVERT: C 396 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7826 (mmm) REVERT: C 421 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8542 (pmm) REVERT: C 588 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9011 (tp) REVERT: C 599 CYS cc_start: 0.7441 (t) cc_final: 0.7079 (t) REVERT: C 738 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8752 (tptt) REVERT: C 825 LEU cc_start: 0.5810 (mt) cc_final: 0.5447 (mt) REVERT: C 892 ARG cc_start: 0.8159 (mmp-170) cc_final: 0.7496 (ptp-170) REVERT: D 147 LYS cc_start: 0.5744 (tptp) cc_final: 0.4844 (mptt) REVERT: D 188 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8064 (t0) REVERT: D 230 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8407 (t0) REVERT: D 786 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6608 (t70) REVERT: D 825 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (mm) REVERT: D 930 MET cc_start: 0.8023 (pmm) cc_final: 0.7281 (pmm) REVERT: D 1001 MET cc_start: 0.8546 (tpp) cc_final: 0.8307 (tpp) REVERT: E 16 TYR cc_start: 0.6949 (t80) cc_final: 0.6702 (t80) REVERT: E 47 CYS cc_start: 0.6649 (OUTLIER) cc_final: 0.5961 (t) REVERT: E 67 PHE cc_start: 0.7685 (m-80) cc_final: 0.7423 (m-80) REVERT: E 110 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: F 51 TYR cc_start: 0.8621 (m-10) cc_final: 0.8320 (m-10) REVERT: F 71 LYS cc_start: 0.8701 (tptt) cc_final: 0.8478 (tptt) outliers start: 101 outliers final: 62 residues processed: 325 average time/residue: 0.4299 time to fit residues: 235.4662 Evaluate side-chains 322 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 237 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 15 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 371 optimal weight: 0.4980 chunk 280 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** 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 = 0.3744 r_free = 0.3744 target = 0.105919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067438 restraints weight = 93266.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.068334 restraints weight = 65981.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069016 restraints weight = 49617.963| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34812 Z= 0.105 Angle : 0.535 16.224 46899 Z= 0.269 Chirality : 0.039 0.243 5003 Planarity : 0.003 0.051 5976 Dihedral : 4.490 58.990 4524 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 2.49 % Allowed : 28.44 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 4060 helix: 1.46 (0.11), residues: 2423 sheet: -1.34 (0.37), residues: 176 loop : -1.01 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 919 HIS 0.012 0.001 HIS D 786 PHE 0.024 0.001 PHE B 949 TYR 0.026 0.001 TYR D 888 ARG 0.004 0.000 ARG C 760 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 1724) hydrogen bonds : angle 3.78184 ( 4977) covalent geometry : bond 0.00236 (34812) covalent geometry : angle 0.53498 (46899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 245 time to evaluate : 4.256 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 9 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8699 (tptp) REVERT: A 421 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8657 (mtm) REVERT: A 678 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 744 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8613 (t80) REVERT: A 802 ARG cc_start: 0.8284 (ptt90) cc_final: 0.7831 (tmt-80) REVERT: A 936 MET cc_start: 0.4036 (OUTLIER) cc_final: 0.1998 (ptm) REVERT: A 1004 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6961 (t80) REVERT: B 283 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8958 (tt) REVERT: B 342 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8662 (t) REVERT: B 421 MET cc_start: 0.7691 (pmm) cc_final: 0.7301 (pmm) REVERT: B 460 LEU cc_start: 0.9194 (pp) cc_final: 0.8736 (mm) REVERT: B 517 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7207 (ttp80) REVERT: B 648 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: B 835 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6750 (mp) REVERT: B 838 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5875 (mm) REVERT: B 921 PHE cc_start: 0.3441 (t80) cc_final: 0.3131 (t80) REVERT: C 124 MET cc_start: 0.9047 (mmm) cc_final: 0.8741 (mmm) REVERT: C 134 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7644 (p90) REVERT: C 359 ARG cc_start: 0.8641 (tpt170) cc_final: 0.8237 (tpp-160) REVERT: C 396 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7826 (mmm) REVERT: C 421 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8541 (pmm) REVERT: C 588 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9005 (tp) REVERT: C 599 CYS cc_start: 0.7532 (t) cc_final: 0.7142 (t) REVERT: C 738 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8748 (tptt) REVERT: C 825 LEU cc_start: 0.5810 (mt) cc_final: 0.5440 (mt) REVERT: C 892 ARG cc_start: 0.8243 (mmp-170) cc_final: 0.7580 (ptp-170) REVERT: D 147 LYS cc_start: 0.5780 (tptp) cc_final: 0.4841 (mptt) REVERT: D 188 ASP cc_start: 0.8538 (t0) cc_final: 0.8091 (t0) REVERT: D 230 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8489 (t0) REVERT: D 543 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: D 786 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.5553 (t-90) REVERT: D 930 MET cc_start: 0.8078 (pmm) cc_final: 0.7356 (pmm) REVERT: D 936 MET cc_start: 0.3657 (mtt) cc_final: 0.3236 (mtp) REVERT: E 16 TYR cc_start: 0.6973 (t80) cc_final: 0.6546 (t80) REVERT: E 47 CYS cc_start: 0.6685 (OUTLIER) cc_final: 0.5943 (t) REVERT: E 67 PHE cc_start: 0.7732 (m-80) cc_final: 0.7481 (m-80) REVERT: E 110 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: F 51 TYR cc_start: 0.8630 (m-10) cc_final: 0.8326 (m-10) outliers start: 93 outliers final: 61 residues processed: 320 average time/residue: 0.5522 time to fit residues: 303.4685 Evaluate side-chains 315 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 234 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 29 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 332 optimal weight: 0.0670 chunk 261 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 214 optimal weight: 0.4980 chunk 262 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 365 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068093 restraints weight = 92721.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.068982 restraints weight = 61832.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068912 restraints weight = 45328.788| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34812 Z= 0.106 Angle : 0.539 15.102 46899 Z= 0.270 Chirality : 0.039 0.306 5003 Planarity : 0.003 0.052 5976 Dihedral : 4.410 56.928 4521 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 2.30 % Allowed : 28.92 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 4060 helix: 1.47 (0.11), residues: 2424 sheet: -1.31 (0.37), residues: 176 loop : -1.01 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 919 HIS 0.003 0.001 HIS B 128 PHE 0.019 0.001 PHE D 839 TYR 0.026 0.001 TYR D 888 ARG 0.004 0.000 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 1724) hydrogen bonds : angle 3.78409 ( 4977) covalent geometry : bond 0.00241 (34812) covalent geometry : angle 0.53930 (46899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 236 time to evaluate : 7.725 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 9 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8706 (tptp) REVERT: A 421 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8654 (mtm) REVERT: A 678 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7766 (t80) REVERT: A 744 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8639 (t80) REVERT: A 802 ARG cc_start: 0.8318 (ptt90) cc_final: 0.7873 (tmt-80) REVERT: A 936 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.1982 (ptm) REVERT: A 1004 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6881 (t80) REVERT: B 283 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8933 (tt) REVERT: B 342 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8642 (t) REVERT: B 421 MET cc_start: 0.7706 (pmm) cc_final: 0.7378 (pmm) REVERT: B 460 LEU cc_start: 0.9263 (pp) cc_final: 0.8852 (mm) REVERT: B 517 ARG cc_start: 0.7893 (ptt-90) cc_final: 0.7271 (ttp80) REVERT: B 648 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: B 838 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5801 (mm) REVERT: B 921 PHE cc_start: 0.3446 (t80) cc_final: 0.3139 (t80) REVERT: B 989 LYS cc_start: 0.9321 (ptmm) cc_final: 0.8976 (tptt) REVERT: C 124 MET cc_start: 0.9051 (mmm) cc_final: 0.8741 (mmm) REVERT: C 134 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7625 (p90) REVERT: C 326 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8582 (ptt180) REVERT: C 359 ARG cc_start: 0.8713 (tpt170) cc_final: 0.8083 (tpp-160) REVERT: C 396 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7871 (mmm) REVERT: C 421 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8523 (pmm) REVERT: C 588 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8966 (tp) REVERT: C 599 CYS cc_start: 0.7539 (t) cc_final: 0.7156 (t) REVERT: C 738 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8742 (tptt) REVERT: C 825 LEU cc_start: 0.5801 (mt) cc_final: 0.5434 (mt) REVERT: C 892 ARG cc_start: 0.8249 (mmp-170) cc_final: 0.7586 (ptp-170) REVERT: D 147 LYS cc_start: 0.5816 (tptp) cc_final: 0.4911 (mptt) REVERT: D 188 ASP cc_start: 0.8559 (t0) cc_final: 0.8108 (t0) REVERT: D 230 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8516 (t0) REVERT: D 543 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: D 786 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.5771 (t-90) REVERT: D 930 MET cc_start: 0.8067 (pmm) cc_final: 0.7357 (pmm) REVERT: D 936 MET cc_start: 0.3675 (mtt) cc_final: 0.3244 (mtp) REVERT: D 1001 MET cc_start: 0.8325 (tpp) cc_final: 0.8122 (tpp) REVERT: E 16 TYR cc_start: 0.7010 (t80) cc_final: 0.6583 (t80) REVERT: E 47 CYS cc_start: 0.6727 (OUTLIER) cc_final: 0.5973 (t) REVERT: E 67 PHE cc_start: 0.7772 (m-80) cc_final: 0.7530 (m-80) REVERT: E 110 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: F 51 TYR cc_start: 0.8642 (m-10) cc_final: 0.8371 (m-10) outliers start: 86 outliers final: 60 residues processed: 307 average time/residue: 0.5673 time to fit residues: 298.8790 Evaluate side-chains 313 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 233 time to evaluate : 6.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 TYR Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 953 LYS Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 786 HIS Chi-restraints excluded: chain D residue 837 PHE Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 95 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN B 786 HIS ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 HIS ** D 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.067197 restraints weight = 93184.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.068388 restraints weight = 67756.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.068696 restraints weight = 46525.164| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34812 Z= 0.116 Angle : 0.552 15.092 46899 Z= 0.274 Chirality : 0.040 0.301 5003 Planarity : 0.003 0.052 5976 Dihedral : 4.341 57.546 4519 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 2.43 % Allowed : 28.84 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 4060 helix: 1.49 (0.11), residues: 2420 sheet: -1.33 (0.37), residues: 176 loop : -1.00 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 919 HIS 0.003 0.001 HIS B 128 PHE 0.028 0.001 PHE A 301 TYR 0.026 0.001 TYR D 888 ARG 0.004 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 1724) hydrogen bonds : angle 3.79954 ( 4977) covalent geometry : bond 0.00268 (34812) covalent geometry : angle 0.55243 (46899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10817.21 seconds wall clock time: 195 minutes 26.04 seconds (11726.04 seconds total)