Starting phenix.real_space_refine on Thu Dec 26 05:50:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0w_16373/12_2024/8c0w_16373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0w_16373/12_2024/8c0w_16373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c0w_16373/12_2024/8c0w_16373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0w_16373/12_2024/8c0w_16373.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0w_16373/12_2024/8c0w_16373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0w_16373/12_2024/8c0w_16373.cif" } resolution = 4.7 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= 0.001 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 10 5.21 5 S 195 5.16 5 C 27229 2.51 5 N 7349 2.21 5 O 8275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 43092 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8003 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 33} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6215 Classifications: {'peptide': 821} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 29, 'TRANS': 791} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8003 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 33} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6215 Classifications: {'peptide': 821} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 29, 'TRANS': 791} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "E" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8003 Classifications: {'peptide': 1030} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 33} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "F" Number of atoms: 6234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6234 Classifications: {'peptide': 823} Incomplete info: {'backbone_only': 72} Link IDs: {'PTRANS': 29, 'TRANS': 793} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 24.59, per 1000 atoms: 0.57 Number of scatterers: 43092 At special positions: 0 Unit cell: (191.08, 185.64, 141.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 195 16.00 P 34 15.00 Mg 10 11.99 O 8275 8.00 N 7349 7.00 C 27229 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.62 Conformation dependent library (CDL) restraints added in 5.5 seconds 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9928 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 48 sheets defined 40.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 91 through 94 removed outlier: 3.725A pdb=" N VAL A 94 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 118 through 130 removed outlier: 4.022A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.568A pdb=" N SER A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 4.140A pdb=" N HIS A 303 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 324 through 340 removed outlier: 3.883A pdb=" N ASN A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.747A pdb=" N ALA A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 433 through 439 removed outlier: 4.137A pdb=" N TYR A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 471 removed outlier: 3.590A pdb=" N ARG A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 Processing helix chain 'A' and resid 521 through 535 removed outlier: 4.385A pdb=" N TYR A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 562 through 587 removed outlier: 4.953A pdb=" N LEU A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.798A pdb=" N ASN A 601 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 620 through 633 removed outlier: 3.768A pdb=" N LEU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 654 through 662 removed outlier: 3.865A pdb=" N LEU A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'A' and resid 702 through 721 Processing helix chain 'A' and resid 730 through 734 Processing helix chain 'A' and resid 738 through 754 Proline residue: A 751 - end of helix Processing helix chain 'A' and resid 755 through 758 Processing helix chain 'A' and resid 777 through 789 removed outlier: 3.837A pdb=" N MET A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 4.183A pdb=" N LEU A 801 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 823 removed outlier: 3.554A pdb=" N ARG A 814 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 837 Processing helix chain 'A' and resid 848 through 864 removed outlier: 3.811A pdb=" N VAL A 854 " --> pdb=" O MET A 850 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.867A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 removed outlier: 3.924A pdb=" N LEU A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.999A pdb=" N ALA A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 972 removed outlier: 3.762A pdb=" N LYS A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 981 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.805A pdb=" N PHE A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.976A pdb=" N ASN A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.560A pdb=" N SER B 263 " --> pdb=" O LYS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.888A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 322 removed outlier: 3.524A pdb=" N ILE B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 322' Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.793A pdb=" N SER B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.609A pdb=" N VAL B 391 " --> pdb=" O ASN B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 4.530A pdb=" N ASP B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 438 through 447 removed outlier: 3.918A pdb=" N ASN B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 482 removed outlier: 3.873A pdb=" N LEU B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 removed outlier: 3.639A pdb=" N THR B 497 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 498 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 517 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 548 through 566 removed outlier: 4.228A pdb=" N LYS B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 3.646A pdb=" N LYS B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 removed outlier: 4.029A pdb=" N TYR B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 619 " --> pdb=" O PHE B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 641 through 660 Processing helix chain 'B' and resid 669 through 675 Processing helix chain 'B' and resid 676 through 678 No H-bonds generated for 'chain 'B' and resid 676 through 678' Processing helix chain 'B' and resid 703 through 719 removed outlier: 3.793A pdb=" N TRP B 715 " --> pdb=" O GLU B 711 " (cutoff:3.500A) Proline residue: B 716 - end of helix Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.735A pdb=" N LEU B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 4.150A pdb=" N GLN B 777 " --> pdb=" O GLY B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 815 through 825 removed outlier: 4.169A pdb=" N ASN B 819 " --> pdb=" O ASP B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 867 through 880 removed outlier: 3.719A pdb=" N LEU B 871 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 905 removed outlier: 4.011A pdb=" N ILE B 901 " --> pdb=" O ASP B 897 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 938 removed outlier: 4.473A pdb=" N ASP B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 967 removed outlier: 4.103A pdb=" N LEU B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 995 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1006 through 1019 removed outlier: 3.891A pdb=" N VAL B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B1015 " --> pdb=" O LYS B1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.173A pdb=" N GLU C 32 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 91 through 94 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 118 through 131 removed outlier: 3.884A pdb=" N GLN C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.772A pdb=" N ILE C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 removed outlier: 4.008A pdb=" N SER C 323 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 342 removed outlier: 4.181A pdb=" N ASN C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C 330 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.644A pdb=" N HIS C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 434 through 439 Processing helix chain 'C' and resid 451 through 470 removed outlier: 3.680A pdb=" N SER C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 501 removed outlier: 3.515A pdb=" N VAL C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 535 removed outlier: 4.215A pdb=" N ASN C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 562 through 587 removed outlier: 3.552A pdb=" N PHE C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 610 Processing helix chain 'C' and resid 620 through 632 removed outlier: 4.293A pdb=" N ARG C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 654 through 662 Processing helix chain 'C' and resid 666 through 689 Processing helix chain 'C' and resid 702 through 721 removed outlier: 3.947A pdb=" N THR C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 734 Processing helix chain 'C' and resid 737 through 749 Processing helix chain 'C' and resid 779 through 789 removed outlier: 3.626A pdb=" N LYS C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 812 removed outlier: 4.147A pdb=" N ALA C 811 " --> pdb=" O GLY C 807 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 812 " --> pdb=" O GLU C 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 807 through 812' Processing helix chain 'C' and resid 812 through 823 Processing helix chain 'C' and resid 832 through 837 Processing helix chain 'C' and resid 848 through 862 removed outlier: 3.774A pdb=" N ARG C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 883 Processing helix chain 'C' and resid 906 through 916 Processing helix chain 'C' and resid 926 through 934 removed outlier: 3.575A pdb=" N LEU C 930 " --> pdb=" O LYS C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 971 removed outlier: 3.768A pdb=" N TYR C 944 " --> pdb=" O GLY C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 986 Processing helix chain 'C' and resid 999 through 1008 Processing helix chain 'C' and resid 1013 through 1027 removed outlier: 4.401A pdb=" N HIS C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR C1020 " --> pdb=" O GLU C1016 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C1023 " --> pdb=" O HIS C1019 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C1027 " --> pdb=" O VAL C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 401 through 411 removed outlier: 3.576A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'D' and resid 467 through 479 Processing helix chain 'D' and resid 499 through 517 Processing helix chain 'D' and resid 526 through 532 removed outlier: 4.314A pdb=" N LEU D 530 " --> pdb=" O ASN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 566 removed outlier: 3.648A pdb=" N PHE D 556 " --> pdb=" O LYS D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 591 Processing helix chain 'D' and resid 604 through 617 removed outlier: 3.789A pdb=" N ALA D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 610 " --> pdb=" O HIS D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 637 removed outlier: 4.281A pdb=" N GLU D 636 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 658 removed outlier: 3.557A pdb=" N LEU D 658 " --> pdb=" O TYR D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.752A pdb=" N SER D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 675 " --> pdb=" O PHE D 671 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 676 " --> pdb=" O SER D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 685 removed outlier: 4.291A pdb=" N GLY D 685 " --> pdb=" O ALA D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 714 removed outlier: 3.523A pdb=" N LEU D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 719 removed outlier: 5.268A pdb=" N TYR D 719 " --> pdb=" O PRO D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 726 removed outlier: 4.216A pdb=" N VAL D 724 " --> pdb=" O GLU D 720 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN D 725 " --> pdb=" O PRO D 721 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 720 through 726' Processing helix chain 'D' and resid 743 through 753 removed outlier: 3.730A pdb=" N SER D 749 " --> pdb=" O THR D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 767 Processing helix chain 'D' and resid 778 through 789 Processing helix chain 'D' and resid 798 through 803 Processing helix chain 'D' and resid 812 through 822 removed outlier: 3.644A pdb=" N ARG D 816 " --> pdb=" O GLY D 812 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 878 Processing helix chain 'D' and resid 902 through 909 removed outlier: 4.588A pdb=" N GLY D 907 " --> pdb=" O LYS D 904 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D 909 " --> pdb=" O ALA D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 932 Processing helix chain 'D' and resid 956 through 970 removed outlier: 4.278A pdb=" N LEU D 960 " --> pdb=" O GLU D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 997 removed outlier: 4.210A pdb=" N ASP D 992 " --> pdb=" O THR D 989 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU D 994 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1016 removed outlier: 3.906A pdb=" N TYR D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 27 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 118 through 131 removed outlier: 3.554A pdb=" N GLN E 122 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.620A pdb=" N ALA E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 239 through 243 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.907A pdb=" N ILE E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 324 removed outlier: 4.030A pdb=" N GLN E 324 " --> pdb=" O TRP E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 341 Processing helix chain 'E' and resid 374 through 382 Processing helix chain 'E' and resid 434 through 439 Processing helix chain 'E' and resid 451 through 465 removed outlier: 3.984A pdb=" N ARG E 455 " --> pdb=" O PHE E 451 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 463 " --> pdb=" O ASN E 459 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 501 removed outlier: 4.002A pdb=" N VAL E 493 " --> pdb=" O LYS E 489 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS E 498 " --> pdb=" O ARG E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.600A pdb=" N GLY E 527 " --> pdb=" O SER E 523 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 532 " --> pdb=" O TYR E 528 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 553 Processing helix chain 'E' and resid 562 through 587 removed outlier: 3.938A pdb=" N THR E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'E' and resid 603 through 608 Processing helix chain 'E' and resid 620 through 633 Processing helix chain 'E' and resid 633 through 639 Processing helix chain 'E' and resid 654 through 660 removed outlier: 3.625A pdb=" N SER E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 689 removed outlier: 3.894A pdb=" N ILE E 673 " --> pdb=" O ASP E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 714 Processing helix chain 'E' and resid 740 through 745 removed outlier: 3.992A pdb=" N LEU E 745 " --> pdb=" O LYS E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 750 Processing helix chain 'E' and resid 777 through 790 removed outlier: 3.525A pdb=" N ALA E 782 " --> pdb=" O LYS E 778 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS E 783 " --> pdb=" O THR E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 823 removed outlier: 3.740A pdb=" N ALA E 823 " --> pdb=" O LYS E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 836 Processing helix chain 'E' and resid 853 through 858 Processing helix chain 'E' and resid 859 through 868 Processing helix chain 'E' and resid 879 through 883 Processing helix chain 'E' and resid 907 through 917 Processing helix chain 'E' and resid 928 through 934 Processing helix chain 'E' and resid 941 through 968 removed outlier: 3.540A pdb=" N ALA E 945 " --> pdb=" O ALA E 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 969 through 972 Processing helix chain 'E' and resid 978 through 987 removed outlier: 5.117A pdb=" N ASP E 984 " --> pdb=" O ARG E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 998 Processing helix chain 'E' and resid 999 through 1006 removed outlier: 4.043A pdb=" N LYS E1003 " --> pdb=" O GLU E 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 1015 through 1028 removed outlier: 3.691A pdb=" N HIS E1019 " --> pdb=" O ALA E1015 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN E1026 " --> pdb=" O ALA E1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 4.282A pdb=" N PHE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 351 Processing helix chain 'F' and resid 363 through 365 No H-bonds generated for 'chain 'F' and resid 363 through 365' Processing helix chain 'F' and resid 387 through 389 No H-bonds generated for 'chain 'F' and resid 387 through 389' Processing helix chain 'F' and resid 399 through 410 Processing helix chain 'F' and resid 438 through 449 removed outlier: 3.574A pdb=" N GLU F 442 " --> pdb=" O SER F 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 448 " --> pdb=" O VAL F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 480 removed outlier: 3.834A pdb=" N LYS F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 494 Processing helix chain 'F' and resid 499 through 517 Processing helix chain 'F' and resid 526 through 532 removed outlier: 4.127A pdb=" N LEU F 530 " --> pdb=" O ASN F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 547 Processing helix chain 'F' and resid 548 through 568 removed outlier: 3.610A pdb=" N LYS F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 removed outlier: 4.155A pdb=" N ILE F 584 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 591 removed outlier: 4.085A pdb=" N PHE F 589 " --> pdb=" O ASN F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 619 Processing helix chain 'F' and resid 630 through 637 Processing helix chain 'F' and resid 641 through 654 Processing helix chain 'F' and resid 654 through 659 Processing helix chain 'F' and resid 670 through 675 Processing helix chain 'F' and resid 695 through 699 Processing helix chain 'F' and resid 705 through 719 Proline residue: F 716 - end of helix Processing helix chain 'F' and resid 720 through 723 Processing helix chain 'F' and resid 744 through 752 removed outlier: 4.093A pdb=" N ALA F 750 " --> pdb=" O LEU F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 768 removed outlier: 3.747A pdb=" N GLU F 766 " --> pdb=" O LYS F 763 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE F 767 " --> pdb=" O GLY F 764 " (cutoff:3.500A) Processing helix chain 'F' and resid 773 through 788 removed outlier: 3.827A pdb=" N ARG F 780 " --> pdb=" O GLU F 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 825 Processing helix chain 'F' and resid 831 through 835 Processing helix chain 'F' and resid 848 through 852 Processing helix chain 'F' and resid 866 through 868 No H-bonds generated for 'chain 'F' and resid 866 through 868' Processing helix chain 'F' and resid 869 through 880 Processing helix chain 'F' and resid 899 through 904 removed outlier: 3.865A pdb=" N GLU F 903 " --> pdb=" O LYS F 899 " (cutoff:3.500A) Processing helix chain 'F' and resid 913 through 917 Processing helix chain 'F' and resid 919 through 930 removed outlier: 3.549A pdb=" N ARG F 927 " --> pdb=" O LYS F 923 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP F 928 " --> pdb=" O SER F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 932 through 937 Processing helix chain 'F' and resid 989 through 999 Processing helix chain 'F' and resid 1005 through 1018 removed outlier: 4.549A pdb=" N LYS F1011 " --> pdb=" O SER F1007 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F1014 " --> pdb=" O VAL F1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69 removed outlier: 8.759A pdb=" N ILE A 66 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 4 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A 68 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 6 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.778A pdb=" N LEU A 34 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 106 removed outlier: 7.176A pdb=" N VAL A 101 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL A 173 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A 103 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP A 175 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 105 " --> pdb=" O ASP A 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 146 removed outlier: 7.060A pdb=" N ILE A 144 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN A 151 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 209 removed outlier: 6.458A pdb=" N ASP A 206 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA A 280 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 208 " --> pdb=" O ALA A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 356 removed outlier: 5.623A pdb=" N TRP A 389 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG A 316 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 removed outlier: 6.495A pdb=" N LEU A 505 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA A 548 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A 507 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 770 removed outlier: 6.166A pdb=" N CYS A 826 " --> pdb=" O PHE A 872 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE A 874 " --> pdb=" O CYS A 826 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 828 " --> pdb=" O ILE A 874 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA A 876 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A 830 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN A 792 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 829 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 794 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 831 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 796 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 219 removed outlier: 4.189A pdb=" N LEU B 292 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N HIS B 289 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER B 236 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS B 245 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 316 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU B 210 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 334 Processing sheet with id=AB5, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.572A pdb=" N LEU B 356 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 485 through 490 removed outlier: 6.803A pdb=" N PHE B 485 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 523 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 487 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASP B 525 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA B 489 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER B 520 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 575 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 522 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER B 577 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 524 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 457 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY B 578 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 459 " --> pdb=" O GLY B 578 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA B 456 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N TRP B 598 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 458 " --> pdb=" O TRP B 598 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 758 through 762 removed outlier: 7.376A pdb=" N CYS B 792 " --> pdb=" O TYR B 835 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU B 837 " --> pdb=" O CYS B 792 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 794 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA B 839 " --> pdb=" O LEU B 794 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE B 796 " --> pdb=" O ALA B 839 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B 738 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 860 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AB9, first strand: chain 'C' and resid 16 through 19 removed outlier: 6.704A pdb=" N CYS C 16 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP C 58 " --> pdb=" O CYS C 16 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 18 " --> pdb=" O ASP C 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 156 removed outlier: 5.152A pdb=" N ILE C 152 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 104 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 138 through 140 removed outlier: 3.530A pdb=" N GLY C 161 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 278 through 280 removed outlier: 8.561A pdb=" N ILE C 278 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP C 206 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA C 280 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU C 208 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 232 through 235 removed outlier: 3.888A pdb=" N SER C 249 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 395 through 396 removed outlier: 4.031A pdb=" N GLN C 311 " --> pdb=" O GLU C 396 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 315 through 316 Processing sheet with id=AC7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AC8, first strand: chain 'C' and resid 503 through 508 Processing sheet with id=AC9, first strand: chain 'C' and resid 647 through 649 removed outlier: 7.054A pdb=" N SER C 648 " --> pdb=" O ILE C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 792 through 795 removed outlier: 6.630A pdb=" N ASN C 792 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE C 829 " --> pdb=" O ASN C 792 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE C 794 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASP C 831 " --> pdb=" O PHE C 794 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE C 874 " --> pdb=" O CYS C 826 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE C 828 " --> pdb=" O ILE C 874 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA C 876 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE C 830 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU C 897 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 769 " --> pdb=" O LEU C 897 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 249 through 250 removed outlier: 4.605A pdb=" N ALA D 308 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER D 218 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE D 290 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG D 217 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 291 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 234 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AD4, first strand: chain 'D' and resid 485 through 490 removed outlier: 6.320A pdb=" N PHE D 485 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 523 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS D 487 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP D 525 " --> pdb=" O LYS D 487 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA D 489 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D 520 " --> pdb=" O ARG D 573 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU D 575 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 522 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N SER D 577 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU D 524 " --> pdb=" O SER D 577 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP D 598 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 734 through 736 removed outlier: 6.889A pdb=" N ILE D 734 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 837 " --> pdb=" O LEU D 794 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 2 through 8 removed outlier: 8.794A pdb=" N ILE E 66 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER E 4 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 68 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 6 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER E 65 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 34 " --> pdb=" O CYS E 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 144 through 146 removed outlier: 5.623A pdb=" N ILE E 144 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE E 152 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 102 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS E 155 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER E 100 " --> pdb=" O CYS E 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 138 through 140 Processing sheet with id=AD9, first strand: chain 'E' and resid 207 through 209 Processing sheet with id=AE1, first strand: chain 'E' and resid 232 through 235 removed outlier: 6.314A pdb=" N ALA E 233 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 350 through 356 removed outlier: 3.555A pdb=" N ASP E 350 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG E 316 " --> pdb=" O THR E 419 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 344 through 347 Processing sheet with id=AE4, first strand: chain 'E' and resid 504 through 507 removed outlier: 6.607A pdb=" N LEU E 505 " --> pdb=" O PHE E 546 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 595 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA E 476 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLY E 594 " --> pdb=" O ALA E 476 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL E 478 " --> pdb=" O GLY E 594 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL E 596 " --> pdb=" O VAL E 478 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU E 480 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 647 through 648 Processing sheet with id=AE6, first strand: chain 'E' and resid 874 through 875 removed outlier: 3.734A pdb=" N GLY E 875 " --> pdb=" O ILE E 768 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 208 through 219 removed outlier: 8.265A pdb=" N ILE F 290 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG F 217 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N HIS F 289 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER F 236 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS F 245 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS F 212 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN F 316 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU F 210 " --> pdb=" O GLN F 316 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 360 through 362 Processing sheet with id=AE9, first strand: chain 'F' and resid 360 through 362 Processing sheet with id=AF1, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AF2, first strand: chain 'F' and resid 485 through 487 removed outlier: 6.297A pdb=" N PHE F 485 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL F 523 " --> pdb=" O PHE F 485 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS F 487 " --> pdb=" O VAL F 523 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER F 520 " --> pdb=" O ARG F 573 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LEU F 575 " --> pdb=" O SER F 520 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE F 522 " --> pdb=" O LEU F 575 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER F 577 " --> pdb=" O ILE F 522 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU F 524 " --> pdb=" O SER F 577 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE F 457 " --> pdb=" O PHE F 576 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA F 456 " --> pdb=" O SER F 595 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR F 597 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE F 458 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER F 599 " --> pdb=" O ILE F 458 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP F 460 " --> pdb=" O SER F 599 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 837 through 838 1516 hydrogen bonds defined for protein. 4113 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: 20.10 Time building geometry restraints manager: 13.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11697 1.33 - 1.45: 7634 1.45 - 1.58: 24271 1.58 - 1.70: 31 1.70 - 1.82: 288 Bond restraints: 43921 Sorted by residual: bond pdb=" CB GLN C 124 " pdb=" CG GLN C 124 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.56e+00 bond pdb=" CG1 ILE B 734 " pdb=" CD1 ILE B 734 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.87e+00 bond pdb=" CG1 ILE E 744 " pdb=" CD1 ILE E 744 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.65e+00 bond pdb=" CG1 ILE E 627 " pdb=" CD1 ILE E 627 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.69e+00 bond pdb=" CG LEU B 521 " pdb=" CD2 LEU B 521 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.69e+00 ... (remaining 43916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 58248 2.71 - 5.42: 1053 5.42 - 8.13: 91 8.13 - 10.84: 14 10.84 - 13.55: 2 Bond angle restraints: 59408 Sorted by residual: angle pdb=" C ARG A 639 " pdb=" N ASP A 640 " pdb=" CA ASP A 640 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.03e+01 angle pdb=" C ALA C 361 " pdb=" CA ALA C 361 " pdb=" CB ALA C 361 " ideal model delta sigma weight residual 116.54 109.36 7.18 1.15e+00 7.56e-01 3.90e+01 angle pdb=" CA GLN C 124 " pdb=" CB GLN C 124 " pdb=" CG GLN C 124 " ideal model delta sigma weight residual 114.10 124.62 -10.52 2.00e+00 2.50e-01 2.77e+01 angle pdb=" C ARG E 917 " pdb=" N LYS E 918 " pdb=" CA LYS E 918 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ARG E 413 " pdb=" CA ARG E 413 " pdb=" C ARG E 413 " ideal model delta sigma weight residual 108.00 115.36 -7.36 1.48e+00 4.57e-01 2.48e+01 ... (remaining 59403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 25702 31.02 - 62.04: 577 62.04 - 93.06: 126 93.06 - 124.08: 4 124.08 - 155.10: 2 Dihedral angle restraints: 26411 sinusoidal: 10779 harmonic: 15632 Sorted by residual: dihedral pdb=" O2A ADP D1102 " pdb=" O3A ADP D1102 " pdb=" PA ADP D1102 " pdb=" PB ADP D1102 " ideal model delta sinusoidal sigma weight residual 300.00 144.90 155.10 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP F1102 " pdb=" O3A ADP F1102 " pdb=" PA ADP F1102 " pdb=" PB ADP F1102 " ideal model delta sinusoidal sigma weight residual -60.00 86.58 -146.58 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" C4' ADP D1102 " pdb=" C5' ADP D1102 " pdb=" O5' ADP D1102 " pdb=" PA ADP D1102 " ideal model delta sinusoidal sigma weight residual -180.00 -59.44 -120.56 1 2.00e+01 2.50e-03 3.62e+01 ... (remaining 26408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5964 0.087 - 0.174: 626 0.174 - 0.261: 16 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CG LEU A 512 " pdb=" CB LEU A 512 " pdb=" CD1 LEU A 512 " pdb=" CD2 LEU A 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB ILE B 734 " pdb=" CA ILE B 734 " pdb=" CG1 ILE B 734 " pdb=" CG2 ILE B 734 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLN C 124 " pdb=" N GLN C 124 " pdb=" C GLN C 124 " pdb=" CB GLN C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 6605 not shown) Planarity restraints: 7665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 624 " -0.361 9.50e-02 1.11e+02 1.63e-01 1.93e+01 pdb=" NE ARG C 624 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 624 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG C 624 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 624 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 892 " 0.334 9.50e-02 1.11e+02 1.50e-01 1.61e+01 pdb=" NE ARG E 892 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG E 892 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG E 892 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 892 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 469 " 0.288 9.50e-02 1.11e+02 1.30e-01 1.29e+01 pdb=" NE ARG B 469 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 469 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 469 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 469 " 0.001 2.00e-02 2.50e+03 ... (remaining 7662 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 132 2.38 - 3.01: 25904 3.01 - 3.64: 65038 3.64 - 4.27: 91938 4.27 - 4.90: 145044 Nonbonded interactions: 328056 Sorted by model distance: nonbonded pdb=" O1B ATP B1101 " pdb="MG MG B1103 " model vdw 1.748 2.170 nonbonded pdb=" O1B ATP A1101 " pdb="MG MG A1103 " model vdw 1.755 2.170 nonbonded pdb=" O3B ATP B1102 " pdb="MG MG B1104 " model vdw 1.776 2.170 nonbonded pdb=" O3G ATP B1101 " pdb="MG MG B1103 " model vdw 1.800 2.170 nonbonded pdb=" O2B ATP D1101 " pdb="MG MG D1103 " model vdw 1.815 2.170 ... (remaining 328051 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 201 through 1021) selection = (chain 'D' and resid 201 through 1021) selection = (chain 'F' and resid 201 through 1021) } 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: 11.680 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 3.290 Set scattering table: 0.000 Process input model: 99.930 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.004 0.077 43921 Z= 0.288 Angle : 0.888 13.546 59408 Z= 0.491 Chirality : 0.052 0.435 6608 Planarity : 0.009 0.163 7665 Dihedral : 14.885 155.102 16483 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -2.63 (0.10), residues: 5543 helix: -1.79 (0.10), residues: 1711 sheet: -0.96 (0.20), residues: 651 loop : -1.91 (0.11), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 510 HIS 0.019 0.001 HIS D 808 PHE 0.050 0.002 PHE C 583 TYR 0.036 0.005 TYR A 539 ARG 0.031 0.004 ARG C 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 43 TYR cc_start: 0.6607 (m-80) cc_final: 0.6325 (m-80) REVERT: A 108 GLN cc_start: 0.9159 (mt0) cc_final: 0.8759 (tm-30) REVERT: A 120 MET cc_start: 0.7279 (tpt) cc_final: 0.6766 (tpt) REVERT: A 591 THR cc_start: 0.8798 (m) cc_final: 0.8566 (p) REVERT: A 610 MET cc_start: 0.9025 (mmt) cc_final: 0.8822 (mmm) REVERT: A 679 MET cc_start: 0.8872 (ttp) cc_final: 0.8616 (tmm) REVERT: A 781 MET cc_start: 0.9214 (ppp) cc_final: 0.8842 (ppp) REVERT: B 366 GLN cc_start: 0.7871 (mt0) cc_final: 0.7171 (mm-40) REVERT: B 398 MET cc_start: 0.3408 (mmt) cc_final: 0.2456 (mmt) REVERT: B 475 ILE cc_start: 0.9140 (mt) cc_final: 0.8931 (mt) REVERT: B 809 ASP cc_start: 0.6440 (m-30) cc_final: 0.6173 (m-30) REVERT: B 835 TYR cc_start: 0.8345 (m-80) cc_final: 0.8077 (m-10) REVERT: B 850 LEU cc_start: 0.8803 (tp) cc_final: 0.8073 (tp) REVERT: B 888 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7704 (pttt) REVERT: C 244 ASP cc_start: 0.7918 (m-30) cc_final: 0.7613 (t0) REVERT: C 360 MET cc_start: 0.8949 (mmm) cc_final: 0.8608 (mmt) REVERT: C 457 LEU cc_start: 0.9582 (tt) cc_final: 0.9091 (mm) REVERT: C 570 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8834 (tptt) REVERT: C 610 MET cc_start: 0.7842 (ptp) cc_final: 0.7240 (ptp) REVERT: C 746 ASP cc_start: 0.5974 (m-30) cc_final: 0.5457 (m-30) REVERT: C 780 LEU cc_start: 0.9343 (tp) cc_final: 0.9083 (tt) REVERT: C 805 TYR cc_start: 0.7501 (m-80) cc_final: 0.7035 (m-10) REVERT: C 829 PHE cc_start: 0.8854 (t80) cc_final: 0.8316 (t80) REVERT: C 874 ILE cc_start: 0.9571 (pt) cc_final: 0.9326 (pt) REVERT: C 971 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6377 (tt0) REVERT: C 1008 LEU cc_start: 0.8432 (tp) cc_final: 0.7982 (tp) REVERT: D 317 MET cc_start: 0.7978 (tpt) cc_final: 0.7710 (tpt) REVERT: D 837 LEU cc_start: 0.8044 (tp) cc_final: 0.7552 (tp) REVERT: E 1 MET cc_start: 0.8070 (ppp) cc_final: 0.7628 (tpp) REVERT: E 376 ASP cc_start: 0.8287 (m-30) cc_final: 0.7918 (p0) REVERT: E 533 CYS cc_start: 0.8311 (m) cc_final: 0.7951 (m) REVERT: E 549 HIS cc_start: 0.8413 (m90) cc_final: 0.8151 (m90) REVERT: E 805 TYR cc_start: 0.8019 (t80) cc_final: 0.7689 (m-80) REVERT: E 951 MET cc_start: 0.8198 (tmm) cc_final: 0.7976 (tmm) REVERT: E 961 MET cc_start: 0.8898 (mtp) cc_final: 0.7484 (tmm) REVERT: E 995 VAL cc_start: 0.5060 (t) cc_final: 0.4559 (t) REVERT: F 278 PHE cc_start: 0.7296 (m-80) cc_final: 0.7037 (m-80) REVERT: F 290 ILE cc_start: 0.9371 (mt) cc_final: 0.9168 (mm) REVERT: F 317 MET cc_start: 0.5143 (tpp) cc_final: 0.3954 (mmt) REVERT: F 345 ASP cc_start: 0.6689 (m-30) cc_final: 0.6231 (t70) REVERT: F 381 CYS cc_start: 0.7528 (t) cc_final: 0.7219 (m) REVERT: F 383 LEU cc_start: 0.7710 (mt) cc_final: 0.7191 (tp) REVERT: F 474 LEU cc_start: 0.9550 (tp) cc_final: 0.9185 (tp) REVERT: F 635 LEU cc_start: 0.8818 (mm) cc_final: 0.8536 (tp) REVERT: F 661 ASP cc_start: 0.8256 (m-30) cc_final: 0.7336 (t0) REVERT: F 795 PHE cc_start: 0.8456 (t80) cc_final: 0.7401 (t80) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.6004 time to fit residues: 721.2381 Evaluate side-chains 347 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 5.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 468 optimal weight: 30.0000 chunk 420 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 435 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 323 optimal weight: 0.9990 chunk 504 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 535 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN A 969 HIS B 495 HIS B 566 ASN B 820 GLN B 824 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS C 818 GLN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 HIS D 327 ASN D 359 ASN D 483 HIS ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN E 311 GLN E 384 ASN E 569 GLN E 573 ASN E 643 GLN ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43921 Z= 0.223 Angle : 0.745 11.975 59408 Z= 0.390 Chirality : 0.047 0.218 6608 Planarity : 0.005 0.059 7665 Dihedral : 11.679 139.147 6286 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.26 % Allowed : 4.29 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.61 (0.11), residues: 5543 helix: -0.42 (0.12), residues: 1745 sheet: -0.88 (0.19), residues: 642 loop : -1.49 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 715 HIS 0.013 0.002 HIS B 495 PHE 0.034 0.002 PHE A 339 TYR 0.034 0.002 TYR C 13 ARG 0.008 0.001 ARG C 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 475 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9131 (mt0) cc_final: 0.8814 (tm-30) REVERT: A 135 MET cc_start: 0.7814 (mmm) cc_final: 0.7515 (mmm) REVERT: A 407 PHE cc_start: 0.7562 (p90) cc_final: 0.6964 (p90) REVERT: A 610 MET cc_start: 0.8981 (mmt) cc_final: 0.8719 (mmm) REVERT: A 679 MET cc_start: 0.8930 (ttp) cc_final: 0.8541 (tmm) REVERT: A 781 MET cc_start: 0.9200 (ppp) cc_final: 0.8717 (ppp) REVERT: B 398 MET cc_start: 0.3472 (mmt) cc_final: 0.2821 (mmt) REVERT: B 475 ILE cc_start: 0.9222 (mt) cc_final: 0.8833 (mt) REVERT: B 825 MET cc_start: 0.7572 (ttp) cc_final: 0.6767 (tmm) REVERT: B 835 TYR cc_start: 0.8311 (m-80) cc_final: 0.8070 (m-10) REVERT: B 888 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7674 (tttt) REVERT: B 1021 LYS cc_start: 0.7087 (tttt) cc_final: 0.6146 (mptt) REVERT: C 114 MET cc_start: 0.3601 (mmm) cc_final: 0.3236 (mtm) REVERT: C 124 GLN cc_start: 0.8126 (mp10) cc_final: 0.7801 (pm20) REVERT: C 178 GLN cc_start: 0.7352 (tp-100) cc_final: 0.7141 (mp10) REVERT: C 244 ASP cc_start: 0.7717 (m-30) cc_final: 0.7317 (t0) REVERT: C 360 MET cc_start: 0.8812 (mmm) cc_final: 0.8286 (mmt) REVERT: C 457 LEU cc_start: 0.9495 (tt) cc_final: 0.9182 (mm) REVERT: C 492 MET cc_start: 0.9148 (mtp) cc_final: 0.8865 (mtp) REVERT: C 570 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8805 (tptt) REVERT: C 610 MET cc_start: 0.7724 (ptp) cc_final: 0.7185 (ptp) REVERT: C 734 ILE cc_start: 0.7744 (mp) cc_final: 0.7537 (mp) REVERT: C 805 TYR cc_start: 0.7491 (m-80) cc_final: 0.7223 (m-10) REVERT: C 829 PHE cc_start: 0.8860 (t80) cc_final: 0.8385 (t80) REVERT: C 874 ILE cc_start: 0.9559 (pt) cc_final: 0.9154 (mp) REVERT: C 971 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6369 (tt0) REVERT: D 508 MET cc_start: 0.8420 (tmm) cc_final: 0.8061 (tmm) REVERT: D 684 ARG cc_start: 0.7693 (mpp80) cc_final: 0.7447 (ttm170) REVERT: D 711 GLU cc_start: 0.8419 (tt0) cc_final: 0.7750 (tm-30) REVERT: E 1 MET cc_start: 0.7986 (ppp) cc_final: 0.7505 (tpp) REVERT: E 314 ILE cc_start: 0.9171 (tp) cc_final: 0.8847 (pt) REVERT: E 376 ASP cc_start: 0.8167 (m-30) cc_final: 0.7869 (p0) REVERT: E 492 MET cc_start: 0.8063 (mmp) cc_final: 0.7853 (mmm) REVERT: E 510 LEU cc_start: 0.7677 (tp) cc_final: 0.7309 (tp) REVERT: E 511 SER cc_start: 0.8741 (m) cc_final: 0.8428 (t) REVERT: E 801 LEU cc_start: 0.6592 (tp) cc_final: 0.5648 (tt) REVERT: E 805 TYR cc_start: 0.7929 (t80) cc_final: 0.7585 (m-80) REVERT: E 812 ASN cc_start: 0.7760 (m-40) cc_final: 0.7525 (m-40) REVERT: E 851 ASP cc_start: 0.8975 (p0) cc_final: 0.8450 (t70) REVERT: E 853 ILE cc_start: 0.9133 (mm) cc_final: 0.8739 (pt) REVERT: E 951 MET cc_start: 0.8116 (tmm) cc_final: 0.7616 (tmm) REVERT: E 961 MET cc_start: 0.8897 (mtp) cc_final: 0.7497 (tmm) REVERT: F 317 MET cc_start: 0.5343 (tpp) cc_final: 0.4109 (mmt) REVERT: F 474 LEU cc_start: 0.9447 (tp) cc_final: 0.9190 (tp) REVERT: F 661 ASP cc_start: 0.8198 (m-30) cc_final: 0.7211 (t0) REVERT: F 794 LEU cc_start: 0.8658 (mt) cc_final: 0.8445 (mt) REVERT: F 795 PHE cc_start: 0.8558 (t80) cc_final: 0.7054 (t80) outliers start: 12 outliers final: 3 residues processed: 486 average time/residue: 0.5832 time to fit residues: 465.3178 Evaluate side-chains 312 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 309 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 280 optimal weight: 40.0000 chunk 156 optimal weight: 9.9990 chunk 419 optimal weight: 10.0000 chunk 343 optimal weight: 0.0170 chunk 139 optimal weight: 6.9990 chunk 504 optimal weight: 5.9990 chunk 545 optimal weight: 10.0000 chunk 449 optimal weight: 2.9990 chunk 500 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 405 optimal weight: 9.9990 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43921 Z= 0.256 Angle : 0.705 11.271 59408 Z= 0.368 Chirality : 0.046 0.182 6608 Planarity : 0.004 0.060 7665 Dihedral : 11.312 136.237 6286 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.11 % Allowed : 3.73 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.49 (0.11), residues: 5543 helix: -0.20 (0.12), residues: 1733 sheet: -1.01 (0.19), residues: 669 loop : -1.46 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 715 HIS 0.010 0.001 HIS D 808 PHE 0.033 0.002 PHE D 593 TYR 0.029 0.002 TYR C 13 ARG 0.009 0.001 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 412 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9139 (mt0) cc_final: 0.8868 (tm-30) REVERT: A 135 MET cc_start: 0.7901 (mmm) cc_final: 0.7633 (mmm) REVERT: A 234 PHE cc_start: 0.8177 (p90) cc_final: 0.7509 (p90) REVERT: A 407 PHE cc_start: 0.7584 (p90) cc_final: 0.6942 (p90) REVERT: A 512 LEU cc_start: 0.8865 (pp) cc_final: 0.8623 (pp) REVERT: A 610 MET cc_start: 0.9069 (mmt) cc_final: 0.8807 (mmm) REVERT: A 632 LEU cc_start: 0.9547 (mt) cc_final: 0.9033 (tp) REVERT: A 679 MET cc_start: 0.8898 (ttp) cc_final: 0.8523 (tmm) REVERT: A 781 MET cc_start: 0.9213 (ppp) cc_final: 0.8760 (ppp) REVERT: A 797 LYS cc_start: 0.8046 (tttt) cc_final: 0.7631 (tttm) REVERT: A 808 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7039 (tm-30) REVERT: A 961 MET cc_start: 0.7984 (tmm) cc_final: 0.7641 (tmm) REVERT: A 968 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: B 398 MET cc_start: 0.3479 (mmt) cc_final: 0.2944 (mmt) REVERT: B 825 MET cc_start: 0.7969 (ptt) cc_final: 0.7585 (ttp) REVERT: B 835 TYR cc_start: 0.8266 (m-80) cc_final: 0.8051 (m-10) REVERT: B 850 LEU cc_start: 0.8768 (tp) cc_final: 0.8258 (tp) REVERT: C 178 GLN cc_start: 0.7412 (tp-100) cc_final: 0.7172 (mp10) REVERT: C 244 ASP cc_start: 0.7879 (m-30) cc_final: 0.7466 (t0) REVERT: C 360 MET cc_start: 0.8790 (mmm) cc_final: 0.8378 (mmt) REVERT: C 457 LEU cc_start: 0.9508 (tt) cc_final: 0.9220 (mm) REVERT: C 492 MET cc_start: 0.9185 (mtp) cc_final: 0.8891 (mtp) REVERT: C 570 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8813 (tptt) REVERT: C 829 PHE cc_start: 0.8779 (t80) cc_final: 0.8405 (t80) REVERT: C 874 ILE cc_start: 0.9590 (pt) cc_final: 0.9093 (mm) REVERT: C 971 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6312 (tt0) REVERT: D 223 MET cc_start: 0.7159 (mmm) cc_final: 0.6958 (mmm) REVERT: D 622 MET cc_start: 0.8852 (ppp) cc_final: 0.7707 (ppp) REVERT: D 684 ARG cc_start: 0.7738 (mpp80) cc_final: 0.7504 (ttm170) REVERT: D 715 TRP cc_start: 0.7986 (m-10) cc_final: 0.7727 (m-10) REVERT: D 825 MET cc_start: 0.7163 (mpp) cc_final: 0.6944 (mpp) REVERT: E 314 ILE cc_start: 0.9165 (tp) cc_final: 0.8911 (pt) REVERT: E 376 ASP cc_start: 0.8201 (m-30) cc_final: 0.7845 (p0) REVERT: E 511 SER cc_start: 0.8804 (m) cc_final: 0.8572 (t) REVERT: E 812 ASN cc_start: 0.7604 (m-40) cc_final: 0.7360 (t0) REVERT: E 851 ASP cc_start: 0.8975 (p0) cc_final: 0.8444 (t70) REVERT: E 961 MET cc_start: 0.8954 (mtp) cc_final: 0.7590 (tmm) REVERT: F 317 MET cc_start: 0.5421 (tpp) cc_final: 0.4135 (mmt) outliers start: 5 outliers final: 0 residues processed: 417 average time/residue: 0.5385 time to fit residues: 379.2088 Evaluate side-chains 278 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 5.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 498 optimal weight: 9.9990 chunk 379 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 240 optimal weight: 0.0770 chunk 339 optimal weight: 0.2980 chunk 506 optimal weight: 0.9980 chunk 536 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 overall best weight: 3.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN C 369 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 GLN C 597 ASN ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 842 ASN E 976 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 HIS ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43921 Z= 0.190 Angle : 0.655 10.634 59408 Z= 0.338 Chirality : 0.045 0.182 6608 Planarity : 0.004 0.062 7665 Dihedral : 10.839 134.173 6286 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.31 (0.11), residues: 5543 helix: 0.05 (0.12), residues: 1748 sheet: -0.88 (0.19), residues: 678 loop : -1.43 (0.11), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 547 HIS 0.009 0.001 HIS D 808 PHE 0.025 0.001 PHE D 593 TYR 0.030 0.002 TYR C 13 ARG 0.007 0.000 ARG F1013 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 108 GLN cc_start: 0.9133 (mt0) cc_final: 0.8836 (tm-30) REVERT: A 135 MET cc_start: 0.7897 (mmm) cc_final: 0.7630 (mmm) REVERT: A 464 SER cc_start: 0.9097 (m) cc_final: 0.8864 (p) REVERT: A 512 LEU cc_start: 0.8880 (pp) cc_final: 0.8648 (pp) REVERT: A 610 MET cc_start: 0.8975 (mmt) cc_final: 0.8740 (mmm) REVERT: A 632 LEU cc_start: 0.9524 (mt) cc_final: 0.9029 (tp) REVERT: A 781 MET cc_start: 0.9192 (ppp) cc_final: 0.8770 (ppp) REVERT: A 808 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6988 (tm-30) REVERT: A 961 MET cc_start: 0.8146 (tmm) cc_final: 0.7732 (tmm) REVERT: B 398 MET cc_start: 0.3552 (mmt) cc_final: 0.3006 (mmt) REVERT: B 571 ARG cc_start: 0.8742 (mmm160) cc_final: 0.7596 (mmm160) REVERT: B 719 TYR cc_start: 0.7543 (m-10) cc_final: 0.7273 (m-10) REVERT: B 825 MET cc_start: 0.8031 (ptt) cc_final: 0.7663 (ttp) REVERT: B 835 TYR cc_start: 0.8197 (m-80) cc_final: 0.7981 (m-10) REVERT: B 850 LEU cc_start: 0.8772 (tp) cc_final: 0.8180 (tp) REVERT: B 888 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7506 (pttt) REVERT: C 178 GLN cc_start: 0.7499 (tp-100) cc_final: 0.7235 (mp10) REVERT: C 206 ASP cc_start: 0.8141 (m-30) cc_final: 0.7861 (p0) REVERT: C 244 ASP cc_start: 0.7864 (m-30) cc_final: 0.7473 (t0) REVERT: C 314 ILE cc_start: 0.8446 (pt) cc_final: 0.8124 (mm) REVERT: C 360 MET cc_start: 0.8729 (mmm) cc_final: 0.8475 (mmm) REVERT: C 457 LEU cc_start: 0.9504 (tt) cc_final: 0.9241 (mm) REVERT: C 492 MET cc_start: 0.9194 (mtp) cc_final: 0.8912 (mtp) REVERT: C 570 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8832 (tptt) REVERT: C 829 PHE cc_start: 0.8754 (t80) cc_final: 0.8361 (t80) REVERT: C 874 ILE cc_start: 0.9582 (pt) cc_final: 0.9286 (mp) REVERT: C 971 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6222 (tt0) REVERT: D 622 MET cc_start: 0.8964 (ppp) cc_final: 0.7914 (ppp) REVERT: D 715 TRP cc_start: 0.7896 (m-10) cc_final: 0.7649 (m-10) REVERT: D 899 LYS cc_start: 0.5372 (tptt) cc_final: 0.4601 (mmmt) REVERT: E 120 MET cc_start: 0.7752 (tpp) cc_final: 0.7269 (tpp) REVERT: E 314 ILE cc_start: 0.9157 (tp) cc_final: 0.8935 (pt) REVERT: E 376 ASP cc_start: 0.8186 (m-30) cc_final: 0.7883 (p0) REVERT: E 510 LEU cc_start: 0.8008 (tp) cc_final: 0.7663 (tp) REVERT: E 511 SER cc_start: 0.8718 (m) cc_final: 0.8428 (t) REVERT: E 812 ASN cc_start: 0.7749 (m-40) cc_final: 0.7480 (t0) REVERT: E 851 ASP cc_start: 0.8955 (p0) cc_final: 0.8444 (t70) REVERT: E 951 MET cc_start: 0.7744 (tmm) cc_final: 0.7379 (ttt) REVERT: E 961 MET cc_start: 0.8936 (mtp) cc_final: 0.7635 (tmm) REVERT: F 317 MET cc_start: 0.5381 (tpp) cc_final: 0.4015 (mmt) REVERT: F 389 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8530 (pm20) REVERT: F 825 MET cc_start: 0.4759 (tmm) cc_final: 0.4211 (tmm) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.5298 time to fit residues: 379.2791 Evaluate side-chains 280 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 5.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 446 optimal weight: 30.0000 chunk 304 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 399 optimal weight: 0.5980 chunk 221 optimal weight: 0.0470 chunk 457 optimal weight: 8.9990 chunk 370 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 8.9990 chunk 481 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN C 856 GLN ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 GLN ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 43921 Z= 0.163 Angle : 0.639 10.413 59408 Z= 0.326 Chirality : 0.044 0.178 6608 Planarity : 0.004 0.064 7665 Dihedral : 10.474 131.484 6286 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.20 (0.11), residues: 5543 helix: 0.20 (0.12), residues: 1761 sheet: -0.77 (0.19), residues: 697 loop : -1.41 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 547 HIS 0.009 0.001 HIS D 808 PHE 0.020 0.001 PHE D 593 TYR 0.028 0.001 TYR C 13 ARG 0.008 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 76 MET cc_start: 0.5439 (mmp) cc_final: 0.4886 (pmm) REVERT: A 108 GLN cc_start: 0.9122 (mt0) cc_final: 0.8835 (tm-30) REVERT: A 135 MET cc_start: 0.7810 (mmm) cc_final: 0.7563 (mmm) REVERT: A 158 PHE cc_start: 0.8367 (m-80) cc_final: 0.8092 (t80) REVERT: A 512 LEU cc_start: 0.8935 (pp) cc_final: 0.8596 (pp) REVERT: A 591 THR cc_start: 0.8410 (p) cc_final: 0.8105 (p) REVERT: A 632 LEU cc_start: 0.9516 (mt) cc_final: 0.8941 (tp) REVERT: A 781 MET cc_start: 0.9176 (ppp) cc_final: 0.8794 (ppp) REVERT: A 864 MET cc_start: 0.7667 (ttm) cc_final: 0.7452 (ttp) REVERT: A 961 MET cc_start: 0.8209 (tmm) cc_final: 0.7762 (tmm) REVERT: A 998 MET cc_start: 0.3243 (ttm) cc_final: 0.2858 (ttm) REVERT: B 398 MET cc_start: 0.3510 (mmt) cc_final: 0.2927 (mmt) REVERT: B 528 GLU cc_start: 0.8910 (pm20) cc_final: 0.8401 (tm-30) REVERT: B 571 ARG cc_start: 0.8669 (mmm160) cc_final: 0.7411 (mmm-85) REVERT: B 719 TYR cc_start: 0.7484 (m-10) cc_final: 0.7179 (m-10) REVERT: B 825 MET cc_start: 0.8048 (ptt) cc_final: 0.7669 (ttp) REVERT: B 835 TYR cc_start: 0.8196 (m-80) cc_final: 0.7972 (m-10) REVERT: B 850 LEU cc_start: 0.8788 (tp) cc_final: 0.8207 (tp) REVERT: B 888 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7515 (tttt) REVERT: C 114 MET cc_start: 0.2736 (mmm) cc_final: 0.2290 (mtm) REVERT: C 206 ASP cc_start: 0.8085 (m-30) cc_final: 0.7832 (p0) REVERT: C 244 ASP cc_start: 0.7894 (m-30) cc_final: 0.7513 (t0) REVERT: C 360 MET cc_start: 0.8680 (mmm) cc_final: 0.8262 (mmm) REVERT: C 457 LEU cc_start: 0.9515 (tt) cc_final: 0.9284 (mm) REVERT: C 486 ASN cc_start: 0.9027 (m-40) cc_final: 0.8826 (m110) REVERT: C 492 MET cc_start: 0.9195 (mtp) cc_final: 0.8990 (mtp) REVERT: C 570 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8767 (tptt) REVERT: C 829 PHE cc_start: 0.8765 (t80) cc_final: 0.8402 (t80) REVERT: C 971 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6227 (tt0) REVERT: D 216 LEU cc_start: 0.9069 (tp) cc_final: 0.8836 (tp) REVERT: D 367 ILE cc_start: 0.7355 (pt) cc_final: 0.7098 (mt) REVERT: D 514 CYS cc_start: 0.9152 (m) cc_final: 0.8582 (p) REVERT: D 622 MET cc_start: 0.8982 (ppp) cc_final: 0.7728 (ppp) REVERT: D 715 TRP cc_start: 0.7948 (m-10) cc_final: 0.7643 (m-10) REVERT: D 899 LYS cc_start: 0.5276 (tptt) cc_final: 0.4617 (mmmt) REVERT: E 120 MET cc_start: 0.7730 (tpp) cc_final: 0.7315 (tpp) REVERT: E 314 ILE cc_start: 0.9163 (tp) cc_final: 0.8947 (pt) REVERT: E 376 ASP cc_start: 0.8175 (m-30) cc_final: 0.7908 (p0) REVERT: E 511 SER cc_start: 0.8616 (m) cc_final: 0.8334 (t) REVERT: E 812 ASN cc_start: 0.7729 (m-40) cc_final: 0.7485 (t0) REVERT: E 851 ASP cc_start: 0.8923 (p0) cc_final: 0.8448 (t70) REVERT: E 961 MET cc_start: 0.8938 (mtp) cc_final: 0.7645 (tmm) REVERT: F 317 MET cc_start: 0.5442 (tpp) cc_final: 0.3959 (mmt) REVERT: F 389 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8537 (pm20) REVERT: F 1016 TYR cc_start: 0.6642 (m-10) cc_final: 0.5871 (m-80) outliers start: 2 outliers final: 1 residues processed: 410 average time/residue: 0.5318 time to fit residues: 372.8883 Evaluate side-chains 291 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 5.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 180 optimal weight: 0.0770 chunk 483 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 314 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 536 optimal weight: 20.0000 chunk 445 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 177 optimal weight: 30.0000 chunk 281 optimal weight: 30.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43921 Z= 0.192 Angle : 0.638 10.694 59408 Z= 0.327 Chirality : 0.044 0.212 6608 Planarity : 0.004 0.063 7665 Dihedral : 10.319 131.664 6286 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.14 % Favored : 92.84 % Rotamer: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.16 (0.11), residues: 5543 helix: 0.25 (0.12), residues: 1774 sheet: -0.76 (0.19), residues: 697 loop : -1.41 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 547 HIS 0.008 0.001 HIS D 808 PHE 0.042 0.001 PHE E 583 TYR 0.025 0.001 TYR C 13 ARG 0.008 0.000 ARG C 821 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 5.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 76 MET cc_start: 0.5513 (mmp) cc_final: 0.4890 (pmm) REVERT: A 108 GLN cc_start: 0.9142 (mt0) cc_final: 0.8823 (tm-30) REVERT: A 135 MET cc_start: 0.7864 (mmm) cc_final: 0.7610 (mmm) REVERT: A 387 LEU cc_start: 0.8961 (tt) cc_final: 0.8375 (mt) REVERT: A 512 LEU cc_start: 0.8976 (pp) cc_final: 0.8588 (pp) REVERT: A 632 LEU cc_start: 0.9500 (mt) cc_final: 0.8843 (tp) REVERT: A 637 LEU cc_start: 0.9461 (mt) cc_final: 0.9205 (mt) REVERT: A 781 MET cc_start: 0.9197 (ppp) cc_final: 0.8781 (ppp) REVERT: A 961 MET cc_start: 0.8218 (tmm) cc_final: 0.7740 (tmm) REVERT: B 398 MET cc_start: 0.3512 (mmt) cc_final: 0.3185 (mmt) REVERT: B 528 GLU cc_start: 0.8922 (pm20) cc_final: 0.8421 (tm-30) REVERT: B 571 ARG cc_start: 0.8573 (mmm160) cc_final: 0.7175 (mmm-85) REVERT: B 621 ILE cc_start: 0.8529 (mm) cc_final: 0.8310 (mm) REVERT: B 719 TYR cc_start: 0.7542 (m-10) cc_final: 0.7257 (m-10) REVERT: B 797 ASP cc_start: 0.7201 (t70) cc_final: 0.6757 (t70) REVERT: B 825 MET cc_start: 0.8029 (ptt) cc_final: 0.7648 (ttp) REVERT: B 835 TYR cc_start: 0.8214 (m-80) cc_final: 0.7989 (m-10) REVERT: B 850 LEU cc_start: 0.8763 (tp) cc_final: 0.8047 (tp) REVERT: C 206 ASP cc_start: 0.8123 (m-30) cc_final: 0.7899 (p0) REVERT: C 244 ASP cc_start: 0.7935 (m-30) cc_final: 0.7542 (t0) REVERT: C 256 MET cc_start: 0.7550 (pmm) cc_final: 0.7328 (pmm) REVERT: C 360 MET cc_start: 0.8672 (mmm) cc_final: 0.8184 (mmm) REVERT: C 457 LEU cc_start: 0.9516 (tt) cc_final: 0.9280 (mm) REVERT: C 492 MET cc_start: 0.9196 (mtp) cc_final: 0.8970 (mtp) REVERT: C 560 ASN cc_start: 0.7773 (t0) cc_final: 0.7301 (p0) REVERT: C 570 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8765 (tptt) REVERT: C 610 MET cc_start: 0.7712 (ptp) cc_final: 0.7497 (ptp) REVERT: C 669 ASP cc_start: 0.8058 (m-30) cc_final: 0.7404 (m-30) REVERT: C 746 ASP cc_start: 0.5412 (m-30) cc_final: 0.5124 (m-30) REVERT: C 829 PHE cc_start: 0.8806 (t80) cc_final: 0.8448 (t80) REVERT: C 971 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6282 (tt0) REVERT: D 216 LEU cc_start: 0.9040 (tp) cc_final: 0.8767 (tp) REVERT: D 367 ILE cc_start: 0.7410 (pt) cc_final: 0.7181 (mt) REVERT: D 622 MET cc_start: 0.9012 (ppp) cc_final: 0.7702 (ppp) REVERT: D 715 TRP cc_start: 0.7928 (m-10) cc_final: 0.7640 (m-10) REVERT: D 899 LYS cc_start: 0.5196 (tptt) cc_final: 0.4536 (mmmt) REVERT: E 120 MET cc_start: 0.7778 (tpp) cc_final: 0.7362 (tpp) REVERT: E 314 ILE cc_start: 0.9190 (tp) cc_final: 0.8953 (pt) REVERT: E 376 ASP cc_start: 0.8129 (m-30) cc_final: 0.7853 (p0) REVERT: E 511 SER cc_start: 0.8509 (m) cc_final: 0.8103 (t) REVERT: E 682 THR cc_start: 0.9297 (m) cc_final: 0.8878 (m) REVERT: E 812 ASN cc_start: 0.7734 (m-40) cc_final: 0.7530 (t0) REVERT: E 851 ASP cc_start: 0.8893 (p0) cc_final: 0.8408 (t70) REVERT: E 951 MET cc_start: 0.7609 (tmm) cc_final: 0.7221 (ttt) REVERT: E 961 MET cc_start: 0.8947 (mtp) cc_final: 0.7656 (tmm) REVERT: F 317 MET cc_start: 0.5480 (tpp) cc_final: 0.3905 (mmt) REVERT: F 389 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8520 (pm20) REVERT: F 825 MET cc_start: 0.4607 (tmm) cc_final: 0.4017 (tmm) REVERT: F 1016 TYR cc_start: 0.6625 (m-10) cc_final: 0.5744 (m-80) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.5220 time to fit residues: 348.2679 Evaluate side-chains 271 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 517 optimal weight: 0.8980 chunk 60 optimal weight: 0.0060 chunk 305 optimal weight: 30.0000 chunk 392 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 452 optimal weight: 8.9990 chunk 299 optimal weight: 30.0000 chunk 534 optimal weight: 40.0000 chunk 334 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 overall best weight: 4.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 GLN ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 910 ASN F 205 ASN F 392 GLN ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43921 Z= 0.215 Angle : 0.650 9.244 59408 Z= 0.334 Chirality : 0.045 0.184 6608 Planarity : 0.004 0.061 7665 Dihedral : 10.289 130.364 6286 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.74 % Favored : 92.24 % Rotamer: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.20 (0.11), residues: 5543 helix: 0.20 (0.12), residues: 1779 sheet: -0.70 (0.19), residues: 690 loop : -1.44 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 516 HIS 0.007 0.001 HIS D 808 PHE 0.025 0.002 PHE E 893 TYR 0.032 0.002 TYR E 128 ARG 0.011 0.001 ARG D1013 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 5.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 76 MET cc_start: 0.5839 (mmp) cc_final: 0.4998 (pmm) REVERT: A 108 GLN cc_start: 0.9138 (mt0) cc_final: 0.8849 (tm-30) REVERT: A 135 MET cc_start: 0.7900 (mmm) cc_final: 0.7672 (mmm) REVERT: A 610 MET cc_start: 0.8992 (mmp) cc_final: 0.8574 (mmp) REVERT: A 632 LEU cc_start: 0.9496 (mt) cc_final: 0.8919 (tp) REVERT: A 961 MET cc_start: 0.8254 (tmm) cc_final: 0.7853 (tmm) REVERT: A 998 MET cc_start: 0.4137 (mtp) cc_final: 0.3931 (mtp) REVERT: B 528 GLU cc_start: 0.8972 (pm20) cc_final: 0.8446 (tm-30) REVERT: B 571 ARG cc_start: 0.8595 (mmm160) cc_final: 0.7681 (mmm160) REVERT: B 719 TYR cc_start: 0.7617 (m-10) cc_final: 0.7346 (m-10) REVERT: B 825 MET cc_start: 0.8086 (ptt) cc_final: 0.7673 (ttp) REVERT: B 835 TYR cc_start: 0.8171 (m-80) cc_final: 0.7920 (m-10) REVERT: B 850 LEU cc_start: 0.8684 (tp) cc_final: 0.8112 (tp) REVERT: C 114 MET cc_start: 0.2909 (mmm) cc_final: 0.2675 (mtp) REVERT: C 206 ASP cc_start: 0.8135 (m-30) cc_final: 0.7911 (p0) REVERT: C 244 ASP cc_start: 0.7964 (m-30) cc_final: 0.7577 (t0) REVERT: C 256 MET cc_start: 0.7530 (pmm) cc_final: 0.7297 (pmm) REVERT: C 360 MET cc_start: 0.8673 (mmm) cc_final: 0.8163 (mmm) REVERT: C 457 LEU cc_start: 0.9500 (tt) cc_final: 0.9276 (mm) REVERT: C 560 ASN cc_start: 0.7950 (t0) cc_final: 0.7448 (p0) REVERT: C 570 LYS cc_start: 0.9193 (ttmm) cc_final: 0.8748 (tptt) REVERT: C 610 MET cc_start: 0.7884 (ptp) cc_final: 0.7647 (ptp) REVERT: C 669 ASP cc_start: 0.8024 (m-30) cc_final: 0.7550 (m-30) REVERT: C 805 TYR cc_start: 0.7507 (m-10) cc_final: 0.7304 (m-10) REVERT: C 829 PHE cc_start: 0.8730 (t80) cc_final: 0.8395 (t80) REVERT: C 971 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6360 (tt0) REVERT: D 216 LEU cc_start: 0.8950 (tp) cc_final: 0.8670 (tp) REVERT: D 317 MET cc_start: 0.7101 (mmm) cc_final: 0.6774 (tpt) REVERT: D 509 GLU cc_start: 0.9032 (tt0) cc_final: 0.8780 (tt0) REVERT: D 622 MET cc_start: 0.9060 (ppp) cc_final: 0.7949 (ppp) REVERT: D 715 TRP cc_start: 0.7923 (m-10) cc_final: 0.7612 (m-10) REVERT: D 899 LYS cc_start: 0.5069 (tptt) cc_final: 0.4454 (mmmt) REVERT: E 120 MET cc_start: 0.7825 (tpp) cc_final: 0.7370 (tpp) REVERT: E 314 ILE cc_start: 0.9199 (tp) cc_final: 0.8963 (pt) REVERT: E 376 ASP cc_start: 0.8157 (m-30) cc_final: 0.7852 (p0) REVERT: E 511 SER cc_start: 0.8440 (m) cc_final: 0.8216 (t) REVERT: E 812 ASN cc_start: 0.7745 (m-40) cc_final: 0.7446 (t0) REVERT: E 851 ASP cc_start: 0.8879 (p0) cc_final: 0.8349 (t0) REVERT: E 910 ASN cc_start: 0.6927 (OUTLIER) cc_final: 0.6488 (m-40) REVERT: E 951 MET cc_start: 0.7677 (tmm) cc_final: 0.7231 (ttt) REVERT: E 961 MET cc_start: 0.8981 (mtp) cc_final: 0.7721 (tmm) REVERT: F 317 MET cc_start: 0.5432 (tpp) cc_final: 0.3912 (mmt) REVERT: F 457 ILE cc_start: 0.9384 (mp) cc_final: 0.9134 (mm) REVERT: F 1016 TYR cc_start: 0.6657 (m-10) cc_final: 0.5709 (m-80) outliers start: 2 outliers final: 0 residues processed: 362 average time/residue: 0.5316 time to fit residues: 331.4087 Evaluate side-chains 267 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 330 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 319 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 340 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 420 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 GLN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 HIS ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 GLN ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 43921 Z= 0.156 Angle : 0.634 9.663 59408 Z= 0.320 Chirality : 0.044 0.170 6608 Planarity : 0.004 0.065 7665 Dihedral : 10.003 132.387 6286 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.93 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.08 (0.11), residues: 5543 helix: 0.34 (0.12), residues: 1786 sheet: -0.68 (0.19), residues: 702 loop : -1.39 (0.11), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 547 HIS 0.006 0.001 HIS D 808 PHE 0.044 0.001 PHE E 583 TYR 0.021 0.001 TYR C 13 ARG 0.007 0.000 ARG E 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 5.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.6053 (mmp) cc_final: 0.5194 (pmm) REVERT: A 108 GLN cc_start: 0.9133 (mt0) cc_final: 0.8831 (tm-30) REVERT: A 135 MET cc_start: 0.7823 (mmm) cc_final: 0.7602 (mmm) REVERT: A 313 PHE cc_start: 0.7954 (m-80) cc_final: 0.7165 (m-10) REVERT: A 387 LEU cc_start: 0.8970 (tt) cc_final: 0.8402 (mt) REVERT: A 512 LEU cc_start: 0.8992 (pp) cc_final: 0.8584 (pp) REVERT: A 632 LEU cc_start: 0.9453 (mt) cc_final: 0.8784 (tp) REVERT: A 637 LEU cc_start: 0.9477 (mt) cc_final: 0.9206 (mt) REVERT: A 781 MET cc_start: 0.9187 (ppp) cc_final: 0.8832 (ppp) REVERT: A 961 MET cc_start: 0.8303 (tmm) cc_final: 0.7819 (tmm) REVERT: A 998 MET cc_start: 0.4095 (mtp) cc_final: 0.3793 (mtp) REVERT: B 528 GLU cc_start: 0.8947 (pm20) cc_final: 0.8389 (tm-30) REVERT: B 719 TYR cc_start: 0.7557 (m-10) cc_final: 0.7256 (m-10) REVERT: B 797 ASP cc_start: 0.7317 (t70) cc_final: 0.7020 (t70) REVERT: B 825 MET cc_start: 0.7941 (ptt) cc_final: 0.7432 (ttp) REVERT: B 835 TYR cc_start: 0.8159 (m-80) cc_final: 0.7877 (m-10) REVERT: B 850 LEU cc_start: 0.8578 (tp) cc_final: 0.8077 (tp) REVERT: C 206 ASP cc_start: 0.8128 (m-30) cc_final: 0.7894 (p0) REVERT: C 244 ASP cc_start: 0.7938 (m-30) cc_final: 0.7569 (t0) REVERT: C 337 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8591 (ptpt) REVERT: C 360 MET cc_start: 0.8540 (mmm) cc_final: 0.8065 (mmm) REVERT: C 457 LEU cc_start: 0.9511 (tt) cc_final: 0.9279 (mm) REVERT: C 560 ASN cc_start: 0.7927 (t0) cc_final: 0.7376 (p0) REVERT: C 570 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8726 (tptt) REVERT: C 610 MET cc_start: 0.7794 (ptp) cc_final: 0.7574 (ptp) REVERT: C 669 ASP cc_start: 0.8041 (m-30) cc_final: 0.7677 (m-30) REVERT: C 805 TYR cc_start: 0.7486 (m-10) cc_final: 0.7204 (m-10) REVERT: C 829 PHE cc_start: 0.8669 (t80) cc_final: 0.8349 (t80) REVERT: C 971 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6267 (tt0) REVERT: D 216 LEU cc_start: 0.9001 (tp) cc_final: 0.8732 (tp) REVERT: D 317 MET cc_start: 0.7120 (mmm) cc_final: 0.6777 (tpt) REVERT: D 509 GLU cc_start: 0.9027 (tt0) cc_final: 0.8756 (tt0) REVERT: D 574 VAL cc_start: 0.9582 (p) cc_final: 0.9348 (m) REVERT: D 622 MET cc_start: 0.9035 (ppp) cc_final: 0.7963 (ppp) REVERT: D 845 LEU cc_start: 0.7530 (mt) cc_final: 0.7125 (mt) REVERT: D 899 LYS cc_start: 0.4780 (tptt) cc_final: 0.4330 (mmmt) REVERT: E 120 MET cc_start: 0.7814 (tpp) cc_final: 0.7466 (tpp) REVERT: E 314 ILE cc_start: 0.9186 (tp) cc_final: 0.8984 (pt) REVERT: E 376 ASP cc_start: 0.8063 (m-30) cc_final: 0.7859 (p0) REVERT: E 682 THR cc_start: 0.9255 (m) cc_final: 0.8841 (m) REVERT: E 812 ASN cc_start: 0.7728 (m-40) cc_final: 0.7527 (t0) REVERT: E 850 MET cc_start: 0.6399 (tmm) cc_final: 0.6084 (tmm) REVERT: E 851 ASP cc_start: 0.8781 (p0) cc_final: 0.8314 (t0) REVERT: E 951 MET cc_start: 0.7566 (tmm) cc_final: 0.7126 (ttt) REVERT: E 961 MET cc_start: 0.8929 (mtp) cc_final: 0.7682 (tmm) REVERT: F 317 MET cc_start: 0.5594 (tpp) cc_final: 0.3955 (mmt) REVERT: F 457 ILE cc_start: 0.9332 (mp) cc_final: 0.9054 (mm) REVERT: F 1016 TYR cc_start: 0.6602 (m-10) cc_final: 0.5630 (m-80) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.5635 time to fit residues: 377.0474 Evaluate side-chains 266 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 486 optimal weight: 30.0000 chunk 512 optimal weight: 7.9990 chunk 467 optimal weight: 0.4980 chunk 498 optimal weight: 0.9980 chunk 300 optimal weight: 30.0000 chunk 217 optimal weight: 0.2980 chunk 391 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 450 optimal weight: 10.0000 chunk 471 optimal weight: 0.0980 chunk 496 optimal weight: 9.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 703 GLN C 369 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 43921 Z= 0.161 Angle : 0.634 10.456 59408 Z= 0.320 Chirality : 0.044 0.206 6608 Planarity : 0.004 0.065 7665 Dihedral : 9.861 132.161 6286 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.98 % Favored : 93.00 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.05 (0.11), residues: 5543 helix: 0.35 (0.12), residues: 1786 sheet: -0.62 (0.19), residues: 706 loop : -1.37 (0.11), residues: 3051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 393 HIS 0.006 0.001 HIS D 808 PHE 0.026 0.001 PHE B 278 TYR 0.029 0.001 TYR A 128 ARG 0.008 0.000 ARG E 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 5.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.6030 (mmp) cc_final: 0.5763 (tpp) REVERT: A 108 GLN cc_start: 0.9152 (mt0) cc_final: 0.8846 (tm-30) REVERT: A 135 MET cc_start: 0.7843 (mmm) cc_final: 0.7606 (mmm) REVERT: A 208 GLU cc_start: 0.7640 (tt0) cc_final: 0.7429 (tp30) REVERT: A 313 PHE cc_start: 0.7956 (m-80) cc_final: 0.7170 (m-10) REVERT: A 387 LEU cc_start: 0.9008 (tt) cc_final: 0.8447 (mt) REVERT: A 512 LEU cc_start: 0.9017 (pp) cc_final: 0.8607 (pp) REVERT: A 632 LEU cc_start: 0.9391 (mt) cc_final: 0.8807 (tp) REVERT: A 703 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: A 781 MET cc_start: 0.9207 (ppp) cc_final: 0.8848 (ppp) REVERT: A 797 LYS cc_start: 0.7802 (tttt) cc_final: 0.7499 (tttm) REVERT: A 961 MET cc_start: 0.8305 (tmm) cc_final: 0.8030 (tmm) REVERT: A 998 MET cc_start: 0.4225 (mtp) cc_final: 0.3981 (mtp) REVERT: B 528 GLU cc_start: 0.8978 (pm20) cc_final: 0.8381 (tm-30) REVERT: B 719 TYR cc_start: 0.7494 (m-10) cc_final: 0.7262 (m-10) REVERT: B 763 LYS cc_start: 0.8191 (tppt) cc_final: 0.7671 (mtpt) REVERT: B 825 MET cc_start: 0.7989 (ptt) cc_final: 0.7552 (ttp) REVERT: B 835 TYR cc_start: 0.8124 (m-80) cc_final: 0.7904 (m-10) REVERT: B 850 LEU cc_start: 0.8559 (tp) cc_final: 0.8059 (tp) REVERT: C 114 MET cc_start: 0.2746 (mmm) cc_final: 0.2533 (mtp) REVERT: C 206 ASP cc_start: 0.8069 (m-30) cc_final: 0.7866 (p0) REVERT: C 244 ASP cc_start: 0.7955 (m-30) cc_final: 0.7606 (t0) REVERT: C 337 LYS cc_start: 0.9229 (mmtt) cc_final: 0.8411 (ptpt) REVERT: C 360 MET cc_start: 0.8548 (mmm) cc_final: 0.8059 (mmm) REVERT: C 369 ASN cc_start: 0.6002 (OUTLIER) cc_final: 0.5689 (m-40) REVERT: C 457 LEU cc_start: 0.9535 (tt) cc_final: 0.9288 (mm) REVERT: C 560 ASN cc_start: 0.7877 (t0) cc_final: 0.7304 (p0) REVERT: C 570 LYS cc_start: 0.9195 (ttmm) cc_final: 0.8714 (tptt) REVERT: C 610 MET cc_start: 0.7814 (ptp) cc_final: 0.7600 (ptp) REVERT: C 805 TYR cc_start: 0.7521 (m-10) cc_final: 0.7231 (m-10) REVERT: C 829 PHE cc_start: 0.8654 (t80) cc_final: 0.8325 (t80) REVERT: C 971 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6269 (tt0) REVERT: D 216 LEU cc_start: 0.8978 (tp) cc_final: 0.8678 (tp) REVERT: D 317 MET cc_start: 0.7104 (mmm) cc_final: 0.6766 (tpt) REVERT: D 509 GLU cc_start: 0.9029 (tt0) cc_final: 0.8776 (tt0) REVERT: D 622 MET cc_start: 0.8995 (ppp) cc_final: 0.8403 (ppp) REVERT: D 844 ASP cc_start: 0.8169 (p0) cc_final: 0.7629 (p0) REVERT: D 899 LYS cc_start: 0.4715 (tptt) cc_final: 0.4403 (mmmt) REVERT: E 120 MET cc_start: 0.7817 (tpp) cc_final: 0.7476 (tpt) REVERT: E 314 ILE cc_start: 0.9211 (tp) cc_final: 0.8981 (pt) REVERT: E 376 ASP cc_start: 0.8121 (m-30) cc_final: 0.7843 (p0) REVERT: E 781 MET cc_start: 0.8918 (ppp) cc_final: 0.8697 (ppp) REVERT: E 850 MET cc_start: 0.6381 (tmm) cc_final: 0.6083 (tmm) REVERT: E 851 ASP cc_start: 0.8765 (p0) cc_final: 0.8312 (t0) REVERT: E 951 MET cc_start: 0.7555 (tmm) cc_final: 0.7112 (ttt) REVERT: E 961 MET cc_start: 0.8929 (mtp) cc_final: 0.7687 (tmm) REVERT: F 278 PHE cc_start: 0.7071 (m-80) cc_final: 0.6702 (m-80) REVERT: F 317 MET cc_start: 0.5672 (tpp) cc_final: 0.3979 (mmt) REVERT: F 457 ILE cc_start: 0.9332 (mp) cc_final: 0.9052 (mm) REVERT: F 1016 TYR cc_start: 0.6617 (m-10) cc_final: 0.5651 (m-80) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.5211 time to fit residues: 337.6454 Evaluate side-chains 265 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 5.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 327 optimal weight: 8.9990 chunk 527 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 366 optimal weight: 8.9990 chunk 552 optimal weight: 6.9990 chunk 508 optimal weight: 3.9990 chunk 440 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 340 optimal weight: 20.0000 chunk 269 optimal weight: 40.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 ASN ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43921 Z= 0.210 Angle : 0.651 11.212 59408 Z= 0.331 Chirality : 0.044 0.234 6608 Planarity : 0.004 0.060 7665 Dihedral : 9.924 132.985 6286 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.72 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.08 (0.11), residues: 5543 helix: 0.36 (0.12), residues: 1765 sheet: -0.76 (0.19), residues: 718 loop : -1.36 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 598 HIS 0.006 0.001 HIS D 808 PHE 0.027 0.002 PHE B 615 TYR 0.023 0.002 TYR E 631 ARG 0.007 0.001 ARG E1024 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 5.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 76 MET cc_start: 0.6127 (mmp) cc_final: 0.5191 (pmm) REVERT: A 108 GLN cc_start: 0.9174 (mt0) cc_final: 0.8903 (tm-30) REVERT: A 135 MET cc_start: 0.7994 (mmm) cc_final: 0.7755 (mmm) REVERT: A 313 PHE cc_start: 0.7981 (m-80) cc_final: 0.7285 (m-10) REVERT: A 387 LEU cc_start: 0.9072 (tt) cc_final: 0.8494 (mt) REVERT: A 610 MET cc_start: 0.8151 (mmm) cc_final: 0.7761 (mmm) REVERT: A 632 LEU cc_start: 0.9378 (mt) cc_final: 0.8803 (tp) REVERT: A 961 MET cc_start: 0.8312 (tmm) cc_final: 0.7886 (tmm) REVERT: A 998 MET cc_start: 0.4474 (mtp) cc_final: 0.4274 (mtp) REVERT: B 528 GLU cc_start: 0.9032 (pm20) cc_final: 0.8374 (tm-30) REVERT: B 571 ARG cc_start: 0.8533 (mmm160) cc_final: 0.7628 (mmm160) REVERT: B 719 TYR cc_start: 0.7642 (m-10) cc_final: 0.7342 (m-10) REVERT: B 835 TYR cc_start: 0.8109 (m-80) cc_final: 0.7873 (m-80) REVERT: C 206 ASP cc_start: 0.8144 (m-30) cc_final: 0.7932 (p0) REVERT: C 244 ASP cc_start: 0.7969 (m-30) cc_final: 0.7626 (t0) REVERT: C 321 LEU cc_start: 0.8715 (mt) cc_final: 0.8088 (tp) REVERT: C 360 MET cc_start: 0.8606 (mmm) cc_final: 0.8137 (mmm) REVERT: C 457 LEU cc_start: 0.9520 (tt) cc_final: 0.9187 (mm) REVERT: C 491 THR cc_start: 0.9446 (p) cc_final: 0.9203 (p) REVERT: C 492 MET cc_start: 0.8789 (mtp) cc_final: 0.8467 (mmm) REVERT: C 560 ASN cc_start: 0.7930 (t0) cc_final: 0.7339 (p0) REVERT: C 570 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8739 (tptt) REVERT: C 829 PHE cc_start: 0.8623 (t80) cc_final: 0.8364 (t80) REVERT: C 971 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6276 (tt0) REVERT: D 317 MET cc_start: 0.7194 (mmm) cc_final: 0.6881 (mmp) REVERT: D 474 LEU cc_start: 0.9199 (tp) cc_final: 0.8960 (tt) REVERT: D 509 GLU cc_start: 0.9054 (tt0) cc_final: 0.8768 (tt0) REVERT: D 622 MET cc_start: 0.9023 (ppp) cc_final: 0.8426 (ppp) REVERT: D 715 TRP cc_start: 0.8329 (m-10) cc_final: 0.8069 (m-10) REVERT: D 844 ASP cc_start: 0.8122 (p0) cc_final: 0.7876 (p0) REVERT: D 899 LYS cc_start: 0.4765 (tptt) cc_final: 0.4429 (mmmt) REVERT: E 120 MET cc_start: 0.7871 (tpp) cc_final: 0.7418 (tpp) REVERT: E 314 ILE cc_start: 0.9233 (tp) cc_final: 0.8987 (pt) REVERT: E 376 ASP cc_start: 0.8189 (m-30) cc_final: 0.7880 (p0) REVERT: E 781 MET cc_start: 0.8981 (ppp) cc_final: 0.8756 (ppp) REVERT: E 850 MET cc_start: 0.6423 (tmm) cc_final: 0.6088 (tmm) REVERT: E 851 ASP cc_start: 0.8788 (p0) cc_final: 0.8307 (t0) REVERT: E 951 MET cc_start: 0.7626 (tmm) cc_final: 0.7155 (ttt) REVERT: E 961 MET cc_start: 0.8943 (mtp) cc_final: 0.7683 (tmm) REVERT: F 278 PHE cc_start: 0.7142 (m-80) cc_final: 0.6921 (m-80) REVERT: F 317 MET cc_start: 0.5661 (tpp) cc_final: 0.3774 (mmt) REVERT: F 457 ILE cc_start: 0.9387 (mp) cc_final: 0.9136 (mm) REVERT: F 1016 TYR cc_start: 0.6608 (m-10) cc_final: 0.5618 (m-80) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.5538 time to fit residues: 330.1237 Evaluate side-chains 252 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 5.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 349 optimal weight: 0.2980 chunk 469 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 405 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 440 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 452 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.077676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058848 restraints weight = 253753.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058967 restraints weight = 170871.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059250 restraints weight = 134539.821| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43921 Z= 0.207 Angle : 0.645 11.054 59408 Z= 0.327 Chirality : 0.044 0.216 6608 Planarity : 0.004 0.061 7665 Dihedral : 9.918 133.588 6286 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.49 % Favored : 92.50 % Rotamer: Outliers : 0.02 % Allowed : 0.26 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % 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: -1.14 (0.11), residues: 5543 helix: 0.30 (0.12), residues: 1782 sheet: -0.82 (0.19), residues: 726 loop : -1.40 (0.12), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 598 HIS 0.006 0.001 HIS D 808 PHE 0.022 0.002 PHE B 278 TYR 0.020 0.001 TYR C 631 ARG 0.007 0.001 ARG D1013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9418.49 seconds wall clock time: 174 minutes 32.97 seconds (10472.97 seconds total)