Starting phenix.real_space_refine on Tue Aug 26 23:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0w_16373/08_2025/8c0w_16373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0w_16373/08_2025/8c0w_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c0w_16373/08_2025/8c0w_16373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0w_16373/08_2025/8c0w_16373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c0w_16373/08_2025/8c0w_16373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0w_16373/08_2025/8c0w_16373.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 1, 'PHE:plan': 1} 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, 'ASP:plan': 7, 'ASN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'GLU:plan': 10, 'ARG:plan': 3, 'PHE:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 1, 'PHE:plan': 1} 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, 'ASP:plan': 7, 'ASN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'GLU:plan': 10, 'ARG:plan': 3, 'PHE:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 1, 'PHE:plan': 1} 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, 'ASP:plan': 7, 'ASN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'GLU:plan': 10, 'ARG:plan': 3, 'PHE:plan': 1} 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: 10.38, per 1000 atoms: 0.24 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: 3.85 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.00 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: 11.39 Time building geometry restraints manager: 5.06 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: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 42.870 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.870 ------------------------------------------------------------------------------- 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 : 0.006 0.884 43922 Z= 0.469 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 : 6.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (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 ARG 0.031 0.004 ARG C 624 TYR 0.036 0.005 TYR A 539 PHE 0.050 0.002 PHE C 583 TRP 0.035 0.003 TRP F 510 HIS 0.019 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00438 (43921) covalent geometry : angle 0.88771 (59408) hydrogen bonds : bond 0.16232 ( 1512) hydrogen bonds : angle 7.74925 ( 4113) Misc. bond : bond 0.88402 ( 1) *********************** 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 : 1.698 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: 0.6326 (m-80) REVERT: A 108 GLN cc_start: 0.9159 (mt0) cc_final: 0.8757 (tm-30) REVERT: A 120 MET cc_start: 0.7279 (tpt) cc_final: 0.6767 (tpt) REVERT: A 256 MET cc_start: 0.7797 (mtt) cc_final: 0.7224 (mpp) REVERT: A 591 THR cc_start: 0.8798 (m) cc_final: 0.8564 (p) REVERT: A 610 MET cc_start: 0.9025 (mmt) cc_final: 0.8821 (mmm) REVERT: A 679 MET cc_start: 0.8872 (ttp) cc_final: 0.8612 (tmm) REVERT: A 781 MET cc_start: 0.9214 (ppp) cc_final: 0.8850 (ppp) REVERT: B 366 GLN cc_start: 0.7871 (mt0) cc_final: 0.7167 (mm-40) REVERT: B 398 MET cc_start: 0.3408 (mmt) cc_final: 0.2453 (mmt) REVERT: B 475 ILE cc_start: 0.9140 (mt) cc_final: 0.8936 (mt) REVERT: B 809 ASP cc_start: 0.6440 (m-30) cc_final: 0.6172 (m-30) REVERT: B 835 TYR cc_start: 0.8345 (m-80) cc_final: 0.8084 (m-10) REVERT: B 850 LEU cc_start: 0.8803 (tp) cc_final: 0.8083 (tp) REVERT: B 888 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7705 (pttt) REVERT: C 244 ASP cc_start: 0.7918 (m-30) cc_final: 0.7615 (t0) REVERT: C 360 MET cc_start: 0.8949 (mmm) cc_final: 0.8609 (mmt) REVERT: C 457 LEU cc_start: 0.9582 (tt) cc_final: 0.9090 (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: 0.7250 (ptp) REVERT: C 746 ASP cc_start: 0.5974 (m-30) cc_final: 0.5453 (m-30) REVERT: C 780 LEU cc_start: 0.9343 (tp) cc_final: 0.9082 (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: 0.8318 (t80) REVERT: C 874 ILE cc_start: 0.9571 (pt) cc_final: 0.9327 (pt) REVERT: C 971 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6375 (tt0) REVERT: C 1008 LEU cc_start: 0.8432 (tp) cc_final: 0.7985 (tp) REVERT: D 317 MET cc_start: 0.7978 (tpt) cc_final: 0.7724 (tpt) REVERT: D 707 ASP cc_start: 0.8176 (m-30) cc_final: 0.7952 (p0) REVERT: D 837 LEU cc_start: 0.8044 (tp) cc_final: 0.7590 (tp) REVERT: E 1 MET cc_start: 0.8070 (ppp) cc_final: 0.7630 (tpp) REVERT: E 376 ASP cc_start: 0.8287 (m-30) cc_final: 0.7916 (p0) REVERT: E 533 CYS cc_start: 0.8311 (m) cc_final: 0.7954 (m) REVERT: E 549 HIS cc_start: 0.8413 (m90) cc_final: 0.8150 (m90) REVERT: E 805 TYR cc_start: 0.8019 (t80) cc_final: 0.7690 (m-80) REVERT: E 951 MET cc_start: 0.8198 (tmm) cc_final: 0.7972 (tmm) REVERT: E 961 MET cc_start: 0.8898 (mtp) cc_final: 0.7480 (tmm) REVERT: E 995 VAL cc_start: 0.5060 (t) cc_final: 0.4572 (t) REVERT: F 278 PHE cc_start: 0.7296 (m-80) cc_final: 0.7041 (m-80) REVERT: F 290 ILE cc_start: 0.9371 (mt) cc_final: 0.9170 (mm) REVERT: F 317 MET cc_start: 0.5143 (tpp) cc_final: 0.3951 (mmt) REVERT: F 345 ASP cc_start: 0.6689 (m-30) cc_final: 0.6243 (t70) REVERT: F 381 CYS cc_start: 0.7528 (t) cc_final: 0.7224 (m) REVERT: F 383 LEU cc_start: 0.7710 (mt) cc_final: 0.7194 (tp) REVERT: F 474 LEU cc_start: 0.9550 (tp) cc_final: 0.9184 (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: 0.7397 (t80) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.2242 time to fit residues: 270.8124 Evaluate side-chains 346 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 50.0000 chunk 223 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 475 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 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 697 GLN ** E 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 878 ASN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.080066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061923 restraints weight = 255993.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061732 restraints weight = 177637.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061690 restraints weight = 144895.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.061924 restraints weight = 136779.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.062102 restraints weight = 126480.863| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43922 Z= 0.172 Angle : 0.759 12.223 59408 Z= 0.397 Chirality : 0.047 0.210 6608 Planarity : 0.005 0.059 7665 Dihedral : 11.705 138.832 6286 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.28 % Allowed : 4.48 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.11), residues: 5543 helix: -0.47 (0.12), residues: 1750 sheet: -0.90 (0.19), residues: 642 loop : -1.52 (0.11), residues: 3151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 814 TYR 0.031 0.002 TYR C 13 PHE 0.034 0.002 PHE A 339 TRP 0.036 0.002 TRP D 715 HIS 0.012 0.002 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00363 (43921) covalent geometry : angle 0.75901 (59408) hydrogen bonds : bond 0.04539 ( 1512) hydrogen bonds : angle 5.97486 ( 4113) Misc. bond : bond 0.00276 ( 1) *********************** 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 491 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 478 time to evaluate : 1.743 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: 0.9125 (mt0) cc_final: 0.8796 (tm-30) REVERT: A 135 MET cc_start: 0.8049 (mmm) cc_final: 0.7750 (mmm) REVERT: A 158 PHE cc_start: 0.8377 (m-80) cc_final: 0.8153 (m-80) REVERT: A 256 MET cc_start: 0.8130 (mtt) cc_final: 0.7729 (mpp) REVERT: A 407 PHE cc_start: 0.7743 (p90) cc_final: 0.7145 (p90) REVERT: A 528 TYR cc_start: 0.8551 (t80) cc_final: 0.8261 (t80) REVERT: A 576 MET cc_start: 0.8899 (tpt) cc_final: 0.8648 (tpp) REVERT: A 591 THR cc_start: 0.8957 (m) cc_final: 0.8711 (p) REVERT: A 610 MET cc_start: 0.9179 (mmt) cc_final: 0.8797 (mmm) REVERT: A 679 MET cc_start: 0.9180 (ttp) cc_final: 0.8691 (tmm) REVERT: A 781 MET cc_start: 0.9201 (ppp) cc_final: 0.8763 (ppp) REVERT: A 797 LYS cc_start: 0.8323 (tttt) cc_final: 0.7875 (tttm) REVERT: B 398 MET cc_start: 0.4488 (mmt) cc_final: 0.3699 (mmm) REVERT: B 509 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9120 (pp20) REVERT: B 719 TYR cc_start: 0.8307 (m-10) cc_final: 0.8033 (m-10) REVERT: B 766 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 825 MET cc_start: 0.7964 (ttp) cc_final: 0.7115 (tmm) REVERT: B 835 TYR cc_start: 0.8957 (m-80) cc_final: 0.8723 (m-10) REVERT: B 850 LEU cc_start: 0.8940 (tp) cc_final: 0.8572 (tp) REVERT: B 888 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7804 (tttt) REVERT: B 1021 LYS cc_start: 0.7108 (tttt) cc_final: 0.6160 (mptt) REVERT: C 114 MET cc_start: 0.3483 (mmm) cc_final: 0.3223 (mtm) REVERT: C 244 ASP cc_start: 0.7866 (m-30) cc_final: 0.7574 (t0) REVERT: C 360 MET cc_start: 0.8864 (mmm) cc_final: 0.8276 (mmt) REVERT: C 457 LEU cc_start: 0.9615 (tt) cc_final: 0.9290 (mm) REVERT: C 570 LYS cc_start: 0.9457 (ttmm) cc_final: 0.8998 (tptt) REVERT: C 610 MET cc_start: 0.7813 (ptp) cc_final: 0.7372 (ptp) REVERT: C 701 ILE cc_start: 0.9573 (mp) cc_final: 0.9319 (tp) REVERT: C 734 ILE cc_start: 0.7895 (mp) cc_final: 0.7644 (mp) REVERT: C 805 TYR cc_start: 0.7836 (m-80) cc_final: 0.7631 (m-10) REVERT: C 829 PHE cc_start: 0.9194 (t80) cc_final: 0.8754 (t80) REVERT: C 874 ILE cc_start: 0.9615 (pt) cc_final: 0.9240 (mp) REVERT: C 971 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6642 (tt0) REVERT: C 998 MET cc_start: 0.7965 (tpt) cc_final: 0.7733 (tpt) REVERT: D 508 MET cc_start: 0.8575 (tmm) cc_final: 0.8340 (tmm) REVERT: D 684 ARG cc_start: 0.7904 (mpp80) cc_final: 0.7421 (ttm170) REVERT: E 1 MET cc_start: 0.7969 (ppp) cc_final: 0.7659 (tpp) REVERT: E 314 ILE cc_start: 0.9000 (tp) cc_final: 0.8726 (pt) REVERT: E 360 MET cc_start: 0.9410 (mmp) cc_final: 0.9184 (mmm) REVERT: E 376 ASP cc_start: 0.8609 (m-30) cc_final: 0.8071 (p0) REVERT: E 492 MET cc_start: 0.8560 (mmp) cc_final: 0.8294 (mmm) REVERT: E 510 LEU cc_start: 0.7622 (tp) cc_final: 0.7195 (tp) REVERT: E 511 SER cc_start: 0.8976 (m) cc_final: 0.8769 (t) REVERT: E 801 LEU cc_start: 0.6908 (tp) cc_final: 0.5934 (tt) REVERT: E 805 TYR cc_start: 0.8027 (t80) cc_final: 0.7421 (m-80) REVERT: E 851 ASP cc_start: 0.9226 (p0) cc_final: 0.8571 (t70) REVERT: E 853 ILE cc_start: 0.8987 (mm) cc_final: 0.8677 (pt) REVERT: E 951 MET cc_start: 0.7837 (tmm) cc_final: 0.7422 (tmm) REVERT: E 961 MET cc_start: 0.8936 (mtp) cc_final: 0.7689 (tmm) REVERT: F 278 PHE cc_start: 0.7478 (m-80) cc_final: 0.7124 (m-80) REVERT: F 317 MET cc_start: 0.5642 (tpp) cc_final: 0.4701 (mmt) REVERT: F 345 ASP cc_start: 0.6812 (m-30) cc_final: 0.6591 (t70) REVERT: F 473 GLU cc_start: 0.8459 (tp30) cc_final: 0.8180 (tp30) REVERT: F 474 LEU cc_start: 0.9542 (tp) cc_final: 0.9272 (tp) REVERT: F 661 ASP cc_start: 0.8328 (m-30) cc_final: 0.7286 (t0) outliers start: 13 outliers final: 4 residues processed: 490 average time/residue: 0.2106 time to fit residues: 172.2941 Evaluate side-chains 314 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 309 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 527 optimal weight: 0.0570 chunk 344 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 chunk 353 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 456 optimal weight: 8.9990 chunk 367 optimal weight: 7.9990 chunk 184 optimal weight: 0.3980 chunk 156 optimal weight: 8.9990 overall best weight: 3.4502 ------------------------------------------------------------------------------- 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** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 HIS ** 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** ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 483 HIS ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.079628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061411 restraints weight = 254504.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060905 restraints weight = 190977.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060931 restraints weight = 156572.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061096 restraints weight = 147414.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061318 restraints weight = 133788.797| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43922 Z= 0.144 Angle : 0.684 11.392 59408 Z= 0.355 Chirality : 0.045 0.211 6608 Planarity : 0.004 0.061 7665 Dihedral : 11.227 135.693 6286 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.11), residues: 5543 helix: -0.16 (0.12), residues: 1746 sheet: -0.92 (0.19), residues: 672 loop : -1.45 (0.11), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 624 TYR 0.030 0.002 TYR C 13 PHE 0.036 0.002 PHE D 593 TRP 0.043 0.002 TRP D 297 HIS 0.010 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00311 (43921) covalent geometry : angle 0.68397 (59408) hydrogen bonds : bond 0.04122 ( 1512) hydrogen bonds : angle 5.59683 ( 4113) Misc. bond : bond 0.00014 ( 1) *********************** 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 434 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 430 time to evaluate : 1.750 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 108 GLN cc_start: 0.9118 (mt0) cc_final: 0.8827 (tm-30) REVERT: A 135 MET cc_start: 0.8142 (mmm) cc_final: 0.7860 (mmm) REVERT: A 256 MET cc_start: 0.8226 (mtt) cc_final: 0.7823 (mpp) REVERT: A 407 PHE cc_start: 0.7710 (p90) cc_final: 0.7107 (p90) REVERT: A 512 LEU cc_start: 0.9061 (pp) cc_final: 0.8835 (pp) REVERT: A 528 TYR cc_start: 0.8625 (t80) cc_final: 0.8296 (t80) REVERT: A 576 MET cc_start: 0.9124 (tpt) cc_final: 0.8768 (tpp) REVERT: A 591 THR cc_start: 0.9065 (m) cc_final: 0.8803 (p) REVERT: A 632 LEU cc_start: 0.9737 (mt) cc_final: 0.9153 (tp) REVERT: A 679 MET cc_start: 0.9204 (ttp) cc_final: 0.8673 (tmm) REVERT: A 781 MET cc_start: 0.9207 (ppp) cc_final: 0.8802 (ppp) REVERT: A 808 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6819 (tm-30) REVERT: B 398 MET cc_start: 0.4242 (mmt) cc_final: 0.3572 (mmt) REVERT: B 719 TYR cc_start: 0.8320 (m-10) cc_final: 0.7981 (m-10) REVERT: B 766 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8541 (tm-30) REVERT: B 835 TYR cc_start: 0.8978 (m-80) cc_final: 0.8761 (m-10) REVERT: B 850 LEU cc_start: 0.9249 (tp) cc_final: 0.8763 (tp) REVERT: B 888 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7718 (pttt) REVERT: C 178 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7414 (mp10) REVERT: C 244 ASP cc_start: 0.7954 (m-30) cc_final: 0.7667 (t0) REVERT: C 314 ILE cc_start: 0.8322 (pt) cc_final: 0.8112 (mm) REVERT: C 457 LEU cc_start: 0.9644 (tt) cc_final: 0.9363 (mm) REVERT: C 570 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9010 (tptt) REVERT: C 610 MET cc_start: 0.7951 (ptp) cc_final: 0.7658 (ptp) REVERT: C 701 ILE cc_start: 0.9595 (mp) cc_final: 0.9343 (tp) REVERT: C 829 PHE cc_start: 0.9185 (t80) cc_final: 0.8792 (t80) REVERT: C 874 ILE cc_start: 0.9648 (pt) cc_final: 0.9204 (mm) REVERT: C 971 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6571 (tt0) REVERT: D 216 LEU cc_start: 0.9287 (tp) cc_final: 0.9025 (tp) REVERT: D 292 LEU cc_start: 0.8622 (mp) cc_final: 0.8378 (mp) REVERT: D 514 CYS cc_start: 0.9293 (m) cc_final: 0.9046 (m) REVERT: D 575 LEU cc_start: 0.9577 (tt) cc_final: 0.9295 (mt) REVERT: D 581 LYS cc_start: 0.9259 (ptmm) cc_final: 0.9032 (ptmt) REVERT: D 622 MET cc_start: 0.8936 (ppp) cc_final: 0.7873 (ppp) REVERT: D 684 ARG cc_start: 0.7930 (mpp80) cc_final: 0.7425 (ttm170) REVERT: D 715 TRP cc_start: 0.8186 (m-10) cc_final: 0.7944 (m-10) REVERT: E 120 MET cc_start: 0.7601 (tpp) cc_final: 0.7256 (tpp) REVERT: E 376 ASP cc_start: 0.8614 (m-30) cc_final: 0.8109 (p0) REVERT: E 492 MET cc_start: 0.8501 (mmp) cc_final: 0.8264 (mmm) REVERT: E 851 ASP cc_start: 0.9256 (p0) cc_final: 0.8624 (t70) REVERT: E 944 TYR cc_start: 0.6415 (m-80) cc_final: 0.5751 (m-80) REVERT: E 961 MET cc_start: 0.8934 (mtp) cc_final: 0.7715 (tmm) REVERT: F 278 PHE cc_start: 0.7527 (m-80) cc_final: 0.7117 (m-80) REVERT: F 317 MET cc_start: 0.5670 (tpp) cc_final: 0.4669 (mmt) REVERT: F 473 GLU cc_start: 0.8614 (tp30) cc_final: 0.8098 (tp30) REVERT: F 825 MET cc_start: 0.5104 (tmm) cc_final: 0.4426 (tmm) outliers start: 4 outliers final: 0 residues processed: 433 average time/residue: 0.1968 time to fit residues: 144.9119 Evaluate side-chains 285 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 375 optimal weight: 30.0000 chunk 463 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 497 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 378 optimal weight: 30.0000 chunk 472 optimal weight: 20.0000 chunk 329 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN C 369 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 GLN C 597 ASN C 937 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.077961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059204 restraints weight = 257797.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059093 restraints weight = 195989.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059414 restraints weight = 153300.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059578 restraints weight = 136885.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059761 restraints weight = 127983.100| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 43922 Z= 0.191 Angle : 0.701 10.236 59408 Z= 0.364 Chirality : 0.046 0.192 6608 Planarity : 0.004 0.062 7665 Dihedral : 11.027 131.971 6286 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.11), residues: 5543 helix: -0.08 (0.12), residues: 1744 sheet: -0.93 (0.19), residues: 673 loop : -1.49 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 961 TYR 0.033 0.002 TYR A 279 PHE 0.026 0.002 PHE D 593 TRP 0.025 0.002 TRP F 516 HIS 0.008 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00411 (43921) covalent geometry : angle 0.70076 (59408) hydrogen bonds : bond 0.04056 ( 1512) hydrogen bonds : angle 5.60931 ( 4113) Misc. bond : bond 0.00047 ( 1) *********************** 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 391 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 1.795 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 108 GLN cc_start: 0.9133 (mt0) cc_final: 0.8862 (tm-30) REVERT: A 135 MET cc_start: 0.8183 (mmm) cc_final: 0.7898 (mmm) REVERT: A 256 MET cc_start: 0.8176 (mtt) cc_final: 0.7858 (mpp) REVERT: A 512 LEU cc_start: 0.9076 (pp) cc_final: 0.8856 (pp) REVERT: A 528 TYR cc_start: 0.8513 (t80) cc_final: 0.8223 (t80) REVERT: A 576 MET cc_start: 0.8887 (tpt) cc_final: 0.8595 (tpp) REVERT: A 591 THR cc_start: 0.9053 (m) cc_final: 0.8809 (p) REVERT: A 610 MET cc_start: 0.9132 (mmp) cc_final: 0.8493 (mmp) REVERT: A 632 LEU cc_start: 0.9683 (mt) cc_final: 0.9111 (tp) REVERT: A 781 MET cc_start: 0.9209 (ppp) cc_final: 0.8815 (ppp) REVERT: B 398 MET cc_start: 0.4441 (mmt) cc_final: 0.3634 (mmt) REVERT: B 719 TYR cc_start: 0.8273 (m-10) cc_final: 0.7905 (m-10) REVERT: B 766 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8531 (tm-30) REVERT: B 835 TYR cc_start: 0.8780 (m-80) cc_final: 0.8535 (m-10) REVERT: B 850 LEU cc_start: 0.9208 (tp) cc_final: 0.8751 (tp) REVERT: B 888 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7634 (pttt) REVERT: C 178 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7398 (mp10) REVERT: C 206 ASP cc_start: 0.8372 (m-30) cc_final: 0.8099 (p0) REVERT: C 244 ASP cc_start: 0.8022 (m-30) cc_final: 0.7712 (t0) REVERT: C 387 LEU cc_start: 0.8983 (tt) cc_final: 0.8227 (mt) REVERT: C 457 LEU cc_start: 0.9643 (tt) cc_final: 0.9341 (mm) REVERT: C 462 GLU cc_start: 0.9053 (tp30) cc_final: 0.8831 (tp30) REVERT: C 492 MET cc_start: 0.9061 (mtp) cc_final: 0.8816 (mtp) REVERT: C 570 LYS cc_start: 0.9466 (ttmm) cc_final: 0.8954 (tptt) REVERT: C 829 PHE cc_start: 0.8993 (t80) cc_final: 0.8670 (t80) REVERT: C 874 ILE cc_start: 0.9621 (pt) cc_final: 0.9173 (mm) REVERT: C 971 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6539 (tt0) REVERT: D 216 LEU cc_start: 0.9181 (tp) cc_final: 0.8974 (tp) REVERT: D 317 MET cc_start: 0.7603 (mmm) cc_final: 0.7249 (tpt) REVERT: D 581 LYS cc_start: 0.9228 (ptmm) cc_final: 0.9014 (ptmt) REVERT: D 622 MET cc_start: 0.9124 (ppp) cc_final: 0.8089 (ppp) REVERT: D 684 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7424 (ttm170) REVERT: D 899 LYS cc_start: 0.6403 (tptt) cc_final: 0.5231 (mmmt) REVERT: E 120 MET cc_start: 0.7666 (tpp) cc_final: 0.7336 (tpp) REVERT: E 376 ASP cc_start: 0.8539 (m-30) cc_final: 0.8046 (p0) REVERT: E 510 LEU cc_start: 0.8033 (tp) cc_final: 0.7778 (tp) REVERT: E 851 ASP cc_start: 0.9249 (p0) cc_final: 0.8546 (t70) REVERT: E 917 ARG cc_start: 0.8656 (ttt-90) cc_final: 0.8427 (mtm-85) REVERT: E 944 TYR cc_start: 0.6541 (m-80) cc_final: 0.5845 (m-80) REVERT: E 951 MET cc_start: 0.7493 (tmm) cc_final: 0.7156 (ttt) REVERT: E 961 MET cc_start: 0.8978 (mtp) cc_final: 0.7774 (tmm) REVERT: F 287 GLU cc_start: 0.8712 (mp0) cc_final: 0.8504 (mm-30) REVERT: F 317 MET cc_start: 0.5676 (tpp) cc_final: 0.4621 (mmt) REVERT: F 1016 TYR cc_start: 0.6717 (m-10) cc_final: 0.5769 (m-80) outliers start: 2 outliers final: 1 residues processed: 391 average time/residue: 0.1909 time to fit residues: 127.7441 Evaluate side-chains 283 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 508 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 384 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 507 optimal weight: 7.9990 chunk 333 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 431 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 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 787 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058962 restraints weight = 254295.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058592 restraints weight = 188603.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058769 restraints weight = 154945.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058932 restraints weight = 156773.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059125 restraints weight = 137013.927| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 43922 Z= 0.180 Angle : 0.688 10.557 59408 Z= 0.356 Chirality : 0.046 0.206 6608 Planarity : 0.004 0.061 7665 Dihedral : 10.880 130.371 6286 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.94 % Favored : 92.04 % Rotamer: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.11), residues: 5543 helix: -0.10 (0.12), residues: 1763 sheet: -0.93 (0.19), residues: 680 loop : -1.54 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1013 TYR 0.027 0.002 TYR C 13 PHE 0.030 0.002 PHE D 616 TRP 0.022 0.002 TRP B 547 HIS 0.008 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00387 (43921) covalent geometry : angle 0.68754 (59408) hydrogen bonds : bond 0.03992 ( 1512) hydrogen bonds : angle 5.57121 ( 4113) Misc. bond : bond 0.00045 ( 1) *********************** 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 380 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 1.376 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 108 GLN cc_start: 0.9151 (mt0) cc_final: 0.8873 (tm-30) REVERT: A 135 MET cc_start: 0.8114 (mmm) cc_final: 0.7861 (mmm) REVERT: A 158 PHE cc_start: 0.8212 (m-80) cc_final: 0.7931 (t80) REVERT: A 256 MET cc_start: 0.8146 (mtt) cc_final: 0.7897 (mpp) REVERT: A 528 TYR cc_start: 0.8371 (t80) cc_final: 0.8120 (t80) REVERT: A 576 MET cc_start: 0.8833 (tpt) cc_final: 0.8481 (tpp) REVERT: A 591 THR cc_start: 0.8999 (m) cc_final: 0.8773 (p) REVERT: A 632 LEU cc_start: 0.9607 (mt) cc_final: 0.8907 (tp) REVERT: A 781 MET cc_start: 0.9225 (ppp) cc_final: 0.8832 (ppp) REVERT: B 398 MET cc_start: 0.4288 (mmt) cc_final: 0.3420 (mmt) REVERT: B 719 TYR cc_start: 0.8209 (m-10) cc_final: 0.7829 (m-10) REVERT: B 766 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 835 TYR cc_start: 0.8633 (m-80) cc_final: 0.8363 (m-10) REVERT: C 178 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7342 (mp10) REVERT: C 244 ASP cc_start: 0.8034 (m-30) cc_final: 0.7685 (t0) REVERT: C 256 MET cc_start: 0.7545 (pmm) cc_final: 0.7339 (pmm) REVERT: C 337 LYS cc_start: 0.9152 (mttp) cc_final: 0.8913 (mmtt) REVERT: C 457 LEU cc_start: 0.9622 (tt) cc_final: 0.9330 (mm) REVERT: C 462 GLU cc_start: 0.8981 (tp30) cc_final: 0.8722 (tp30) REVERT: C 492 MET cc_start: 0.8973 (mtp) cc_final: 0.8752 (mtp) REVERT: C 570 LYS cc_start: 0.9426 (ttmm) cc_final: 0.8909 (tptt) REVERT: C 829 PHE cc_start: 0.8766 (t80) cc_final: 0.8508 (t80) REVERT: C 874 ILE cc_start: 0.9591 (pt) cc_final: 0.9289 (mp) REVERT: C 971 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6497 (tt0) REVERT: D 317 MET cc_start: 0.7627 (mmm) cc_final: 0.6904 (tpp) REVERT: D 581 LYS cc_start: 0.9173 (ptmm) cc_final: 0.8957 (ptmt) REVERT: D 622 MET cc_start: 0.9151 (ppp) cc_final: 0.7918 (ppp) REVERT: D 899 LYS cc_start: 0.6149 (tptt) cc_final: 0.5057 (mmmt) REVERT: E 120 MET cc_start: 0.7751 (tpp) cc_final: 0.7416 (tpp) REVERT: E 376 ASP cc_start: 0.8541 (m-30) cc_final: 0.8051 (p0) REVERT: E 851 ASP cc_start: 0.9200 (p0) cc_final: 0.8472 (t70) REVERT: E 961 MET cc_start: 0.8978 (mtp) cc_final: 0.7763 (tmm) REVERT: F 278 PHE cc_start: 0.7338 (m-80) cc_final: 0.7109 (m-80) REVERT: F 317 MET cc_start: 0.5652 (tpp) cc_final: 0.4404 (mmt) REVERT: F 825 MET cc_start: 0.5085 (tmm) cc_final: 0.4320 (tmm) REVERT: F 1016 TYR cc_start: 0.6761 (m-10) cc_final: 0.5695 (m-80) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.1965 time to fit residues: 127.1977 Evaluate side-chains 261 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 534 optimal weight: 6.9990 chunk 372 optimal weight: 20.0000 chunk 330 optimal weight: 0.9980 chunk 402 optimal weight: 0.5980 chunk 313 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 263 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 5.1186 ------------------------------------------------------------------------------- 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** ** A 812 ASN ** 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 205 ASN F 392 GLN F 445 ASN ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 914 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.076961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058034 restraints weight = 254345.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057824 restraints weight = 194639.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058570 restraints weight = 156944.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058653 restraints weight = 131252.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058774 restraints weight = 128842.802| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43922 Z= 0.173 Angle : 0.680 10.086 59408 Z= 0.351 Chirality : 0.045 0.230 6608 Planarity : 0.004 0.062 7665 Dihedral : 10.798 131.845 6286 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.92 % Favored : 92.06 % Rotamer: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.11), residues: 5543 helix: -0.05 (0.12), residues: 1766 sheet: -0.91 (0.19), residues: 684 loop : -1.56 (0.11), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 601 TYR 0.026 0.002 TYR C 13 PHE 0.028 0.002 PHE E 893 TRP 0.051 0.002 TRP D 393 HIS 0.008 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00374 (43921) covalent geometry : angle 0.68042 (59408) hydrogen bonds : bond 0.03885 ( 1512) hydrogen bonds : angle 5.54295 ( 4113) Misc. bond : bond 0.01192 ( 1) *********************** 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 360 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 1.369 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 108 GLN cc_start: 0.9134 (mt0) cc_final: 0.8879 (tm-30) REVERT: A 135 MET cc_start: 0.8145 (mmm) cc_final: 0.7889 (mmm) REVERT: A 256 MET cc_start: 0.8124 (mtt) cc_final: 0.7920 (mpp) REVERT: A 528 TYR cc_start: 0.8448 (t80) cc_final: 0.8199 (t80) REVERT: A 576 MET cc_start: 0.8840 (tpt) cc_final: 0.8589 (tpp) REVERT: A 610 MET cc_start: 0.9084 (mmp) cc_final: 0.8668 (mmm) REVERT: A 781 MET cc_start: 0.9229 (ppp) cc_final: 0.8841 (ppp) REVERT: A 998 MET cc_start: 0.3523 (ttm) cc_final: 0.3180 (ttm) REVERT: B 398 MET cc_start: 0.4305 (mmt) cc_final: 0.3807 (mmm) REVERT: B 719 TYR cc_start: 0.8208 (m-10) cc_final: 0.7831 (m-10) REVERT: B 766 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 797 ASP cc_start: 0.7903 (t0) cc_final: 0.7615 (t0) REVERT: B 835 TYR cc_start: 0.8658 (m-80) cc_final: 0.8369 (m-10) REVERT: C 178 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7219 (mp10) REVERT: C 244 ASP cc_start: 0.8043 (m-30) cc_final: 0.7683 (t0) REVERT: C 256 MET cc_start: 0.7565 (pmm) cc_final: 0.7309 (pmm) REVERT: C 337 LYS cc_start: 0.9168 (mttp) cc_final: 0.8930 (mmtt) REVERT: C 457 LEU cc_start: 0.9625 (tt) cc_final: 0.9337 (mm) REVERT: C 462 GLU cc_start: 0.8995 (tp30) cc_final: 0.8735 (tp30) REVERT: C 560 ASN cc_start: 0.7917 (t0) cc_final: 0.7528 (p0) REVERT: C 570 LYS cc_start: 0.9427 (ttmm) cc_final: 0.8897 (tptt) REVERT: C 829 PHE cc_start: 0.8778 (t80) cc_final: 0.8437 (t80) REVERT: C 850 MET cc_start: 0.8702 (ptm) cc_final: 0.8149 (pmm) REVERT: C 971 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6551 (tt0) REVERT: D 216 LEU cc_start: 0.8987 (tp) cc_final: 0.8741 (tp) REVERT: D 317 MET cc_start: 0.7707 (mmm) cc_final: 0.7210 (tpp) REVERT: D 509 GLU cc_start: 0.8741 (tt0) cc_final: 0.8427 (tt0) REVERT: D 622 MET cc_start: 0.9112 (ppp) cc_final: 0.7876 (ppp) REVERT: D 899 LYS cc_start: 0.6140 (tptt) cc_final: 0.5061 (mmmt) REVERT: E 120 MET cc_start: 0.7772 (tpp) cc_final: 0.7428 (tpp) REVERT: E 376 ASP cc_start: 0.8491 (m-30) cc_final: 0.8073 (p0) REVERT: E 851 ASP cc_start: 0.9227 (p0) cc_final: 0.8474 (t70) REVERT: E 951 MET cc_start: 0.7642 (tmm) cc_final: 0.7070 (ttt) REVERT: E 961 MET cc_start: 0.8992 (mtp) cc_final: 0.7818 (tmm) REVERT: F 317 MET cc_start: 0.5778 (tpp) cc_final: 0.4505 (mmt) REVERT: F 795 PHE cc_start: 0.7667 (t80) cc_final: 0.7200 (t80) REVERT: F 1016 TYR cc_start: 0.6724 (m-10) cc_final: 0.5626 (m-80) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.1979 time to fit residues: 122.2096 Evaluate side-chains 256 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 524 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 274 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 174 optimal weight: 20.0000 chunk 398 optimal weight: 10.0000 chunk 445 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** A 812 ASN ** 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 824 GLN ** 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 = 0.3706 r_free = 0.3706 target = 0.078661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059934 restraints weight = 252880.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060105 restraints weight = 180423.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060348 restraints weight = 140907.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060538 restraints weight = 135294.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060722 restraints weight = 122729.996| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43922 Z= 0.119 Angle : 0.650 10.208 59408 Z= 0.329 Chirality : 0.044 0.170 6608 Planarity : 0.004 0.064 7665 Dihedral : 10.401 133.856 6286 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.04 % Favored : 92.95 % Rotamer: Outliers : 0.02 % Allowed : 1.63 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.11), residues: 5543 helix: 0.16 (0.12), residues: 1766 sheet: -0.67 (0.20), residues: 684 loop : -1.49 (0.11), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1013 TYR 0.023 0.001 TYR C 13 PHE 0.038 0.001 PHE E 583 TRP 0.027 0.001 TRP D 393 HIS 0.007 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00257 (43921) covalent geometry : angle 0.64965 (59408) hydrogen bonds : bond 0.03531 ( 1512) hydrogen bonds : angle 5.24709 ( 4113) Misc. bond : bond 0.00005 ( 1) *********************** 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 378 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.416 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 108 GLN cc_start: 0.9126 (mt0) cc_final: 0.8815 (tm-30) REVERT: A 135 MET cc_start: 0.8101 (mmm) cc_final: 0.7866 (mmm) REVERT: A 256 MET cc_start: 0.8041 (mtt) cc_final: 0.7807 (mpp) REVERT: A 387 LEU cc_start: 0.9056 (tt) cc_final: 0.8548 (mt) REVERT: A 576 MET cc_start: 0.8741 (tpt) cc_final: 0.8471 (tpp) REVERT: A 632 LEU cc_start: 0.9662 (mt) cc_final: 0.8985 (tp) REVERT: A 781 MET cc_start: 0.9205 (ppp) cc_final: 0.8856 (ppp) REVERT: B 398 MET cc_start: 0.3593 (mmt) cc_final: 0.3181 (mmt) REVERT: B 571 ARG cc_start: 0.8735 (mmm160) cc_final: 0.7319 (mmm-85) REVERT: B 622 MET cc_start: 0.7895 (tpt) cc_final: 0.7548 (mmm) REVERT: B 719 TYR cc_start: 0.8193 (m-10) cc_final: 0.7827 (m-10) REVERT: B 763 LYS cc_start: 0.8949 (mmpt) cc_final: 0.8742 (mptt) REVERT: B 766 GLU cc_start: 0.8708 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 797 ASP cc_start: 0.7477 (t0) cc_final: 0.7118 (t0) REVERT: B 835 TYR cc_start: 0.8658 (m-80) cc_final: 0.8348 (m-10) REVERT: C 114 MET cc_start: 0.2551 (mmm) cc_final: 0.2068 (mtm) REVERT: C 178 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7201 (mp10) REVERT: C 244 ASP cc_start: 0.8006 (m-30) cc_final: 0.7692 (t0) REVERT: C 256 MET cc_start: 0.7580 (pmm) cc_final: 0.7351 (pmm) REVERT: C 457 LEU cc_start: 0.9650 (tt) cc_final: 0.9400 (mm) REVERT: C 462 GLU cc_start: 0.9035 (tp30) cc_final: 0.8780 (tp30) REVERT: C 570 LYS cc_start: 0.9413 (ttmm) cc_final: 0.8872 (tptt) REVERT: C 669 ASP cc_start: 0.7676 (m-30) cc_final: 0.7212 (m-30) REVERT: C 829 PHE cc_start: 0.8724 (t80) cc_final: 0.8429 (t80) REVERT: C 971 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6484 (tt0) REVERT: D 216 LEU cc_start: 0.9041 (tp) cc_final: 0.8768 (tp) REVERT: D 317 MET cc_start: 0.7642 (mmm) cc_final: 0.7164 (tpp) REVERT: D 367 ILE cc_start: 0.7476 (pt) cc_final: 0.7181 (mt) REVERT: D 514 CYS cc_start: 0.9100 (m) cc_final: 0.8443 (p) REVERT: D 622 MET cc_start: 0.9090 (ppp) cc_final: 0.7926 (ppp) REVERT: D 899 LYS cc_start: 0.5997 (tptt) cc_final: 0.5003 (mmmt) REVERT: E 120 MET cc_start: 0.7779 (tpp) cc_final: 0.7469 (tpp) REVERT: E 376 ASP cc_start: 0.8532 (m-30) cc_final: 0.8083 (p0) REVERT: E 682 THR cc_start: 0.9301 (m) cc_final: 0.8886 (m) REVERT: E 851 ASP cc_start: 0.9072 (p0) cc_final: 0.8443 (t0) REVERT: E 951 MET cc_start: 0.7488 (tmm) cc_final: 0.7096 (ttt) REVERT: E 961 MET cc_start: 0.8960 (mtp) cc_final: 0.7985 (ppp) REVERT: F 317 MET cc_start: 0.5854 (tpp) cc_final: 0.4599 (mmt) REVERT: F 508 MET cc_start: 0.8725 (tpt) cc_final: 0.8398 (tpt) REVERT: F 511 CYS cc_start: 0.9068 (m) cc_final: 0.8814 (p) REVERT: F 795 PHE cc_start: 0.7556 (t80) cc_final: 0.7013 (t80) REVERT: F 825 MET cc_start: 0.4953 (tmm) cc_final: 0.4205 (tmm) REVERT: F 1016 TYR cc_start: 0.6667 (m-10) cc_final: 0.5623 (m-80) outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.1942 time to fit residues: 126.3499 Evaluate side-chains 259 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 75 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 526 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 493 optimal weight: 20.0000 chunk 368 optimal weight: 5.9990 chunk 478 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** C 856 GLN ** 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 824 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.078027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059869 restraints weight = 254986.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059321 restraints weight = 195480.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059365 restraints weight = 164191.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059568 restraints weight = 158943.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059690 restraints weight = 138335.970| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43922 Z= 0.131 Angle : 0.649 10.190 59408 Z= 0.331 Chirality : 0.045 0.202 6608 Planarity : 0.004 0.064 7665 Dihedral : 10.299 134.928 6286 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.52 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.11), residues: 5543 helix: 0.21 (0.12), residues: 1769 sheet: -0.71 (0.20), residues: 684 loop : -1.50 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1013 TYR 0.021 0.001 TYR C 13 PHE 0.025 0.001 PHE E 583 TRP 0.023 0.001 TRP D 393 HIS 0.006 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00285 (43921) covalent geometry : angle 0.64881 (59408) hydrogen bonds : bond 0.03572 ( 1512) hydrogen bonds : angle 5.25071 ( 4113) Misc. bond : bond 0.00024 ( 1) *********************** 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 350 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9132 (mt0) cc_final: 0.8846 (tm-30) REVERT: A 135 MET cc_start: 0.8162 (mmm) cc_final: 0.7906 (mmm) REVERT: A 256 MET cc_start: 0.8134 (mtt) cc_final: 0.7916 (mpp) REVERT: A 387 LEU cc_start: 0.9070 (tt) cc_final: 0.8583 (mt) REVERT: A 576 MET cc_start: 0.8760 (tpt) cc_final: 0.8528 (tpp) REVERT: A 610 MET cc_start: 0.9067 (mmp) cc_final: 0.8699 (mmp) REVERT: A 632 LEU cc_start: 0.9558 (mt) cc_final: 0.8897 (tp) REVERT: A 781 MET cc_start: 0.9246 (ppp) cc_final: 0.8895 (ppp) REVERT: B 392 GLN cc_start: 0.9110 (mt0) cc_final: 0.8826 (mm110) REVERT: B 398 MET cc_start: 0.3766 (mmt) cc_final: 0.3309 (mmt) REVERT: B 571 ARG cc_start: 0.8715 (mmm160) cc_final: 0.7300 (mmm-85) REVERT: B 719 TYR cc_start: 0.8205 (m-10) cc_final: 0.7824 (m-10) REVERT: B 766 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 797 ASP cc_start: 0.7357 (t0) cc_final: 0.7060 (t0) REVERT: B 825 MET cc_start: 0.8252 (ptt) cc_final: 0.7914 (tmm) REVERT: B 835 TYR cc_start: 0.8607 (m-80) cc_final: 0.8298 (m-10) REVERT: C 178 GLN cc_start: 0.7530 (tp-100) cc_final: 0.7208 (mp10) REVERT: C 244 ASP cc_start: 0.8030 (m-30) cc_final: 0.7733 (t0) REVERT: C 321 LEU cc_start: 0.8780 (mt) cc_final: 0.7950 (tt) REVERT: C 457 LEU cc_start: 0.9648 (tt) cc_final: 0.9408 (mm) REVERT: C 462 GLU cc_start: 0.9024 (tp30) cc_final: 0.8811 (tp30) REVERT: C 492 MET cc_start: 0.8867 (mtp) cc_final: 0.8620 (mtp) REVERT: C 560 ASN cc_start: 0.7745 (t0) cc_final: 0.7322 (p0) REVERT: C 570 LYS cc_start: 0.9367 (ttmm) cc_final: 0.8873 (tptt) REVERT: C 669 ASP cc_start: 0.7625 (m-30) cc_final: 0.7209 (m-30) REVERT: C 829 PHE cc_start: 0.8685 (t80) cc_final: 0.8411 (t80) REVERT: C 971 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6470 (tt0) REVERT: D 216 LEU cc_start: 0.9001 (tp) cc_final: 0.8722 (tp) REVERT: D 317 MET cc_start: 0.7696 (mmm) cc_final: 0.7232 (tpp) REVERT: D 356 LEU cc_start: 0.8077 (pt) cc_final: 0.7806 (pt) REVERT: D 367 ILE cc_start: 0.7521 (pt) cc_final: 0.7287 (mt) REVERT: D 525 ASP cc_start: 0.7610 (t0) cc_final: 0.7396 (t0) REVERT: D 622 MET cc_start: 0.9104 (ppp) cc_final: 0.7915 (ppp) REVERT: D 899 LYS cc_start: 0.5852 (tptt) cc_final: 0.4843 (mmmt) REVERT: E 120 MET cc_start: 0.7823 (tpp) cc_final: 0.7454 (tpp) REVERT: E 376 ASP cc_start: 0.8538 (m-30) cc_final: 0.8113 (p0) REVERT: E 781 MET cc_start: 0.8891 (ppp) cc_final: 0.8626 (ppp) REVERT: E 850 MET cc_start: 0.6141 (tmm) cc_final: 0.5833 (tmm) REVERT: E 851 ASP cc_start: 0.9133 (p0) cc_final: 0.8480 (t0) REVERT: E 951 MET cc_start: 0.7454 (tmm) cc_final: 0.7141 (ttt) REVERT: E 961 MET cc_start: 0.8946 (mtp) cc_final: 0.7765 (tmm) REVERT: F 317 MET cc_start: 0.5783 (tpp) cc_final: 0.4470 (mmt) REVERT: F 508 MET cc_start: 0.8766 (tpt) cc_final: 0.8440 (tpt) REVERT: F 511 CYS cc_start: 0.9091 (m) cc_final: 0.8834 (p) REVERT: F 795 PHE cc_start: 0.7725 (t80) cc_final: 0.7359 (t80) REVERT: F 825 MET cc_start: 0.5008 (tmm) cc_final: 0.4271 (tmm) REVERT: F 1016 TYR cc_start: 0.6741 (m-10) cc_final: 0.5697 (m-80) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1937 time to fit residues: 116.7815 Evaluate side-chains 242 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 184 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 513 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 529 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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** B 968 GLN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 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 910 ASN ** F 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.077112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059633 restraints weight = 259061.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058544 restraints weight = 206875.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059005 restraints weight = 163851.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059197 restraints weight = 140279.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059384 restraints weight = 131362.487| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 43922 Z= 0.166 Angle : 0.678 10.281 59408 Z= 0.347 Chirality : 0.045 0.273 6608 Planarity : 0.004 0.061 7665 Dihedral : 10.297 135.227 6286 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.28 % Favored : 91.70 % Rotamer: Outliers : 0.04 % Allowed : 0.73 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.11), residues: 5543 helix: 0.13 (0.12), residues: 1763 sheet: -0.82 (0.20), residues: 701 loop : -1.55 (0.11), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 821 TYR 0.031 0.002 TYR D 347 PHE 0.023 0.002 PHE C 583 TRP 0.016 0.002 TRP B 547 HIS 0.013 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00362 (43921) covalent geometry : angle 0.67795 (59408) hydrogen bonds : bond 0.03749 ( 1512) hydrogen bonds : angle 5.37881 ( 4113) Misc. bond : bond 0.00038 ( 1) *********************** 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 335 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 1.867 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: A 108 GLN cc_start: 0.9177 (mt0) cc_final: 0.8894 (tm-30) REVERT: A 135 MET cc_start: 0.8224 (mmm) cc_final: 0.7954 (mmm) REVERT: A 256 MET cc_start: 0.8160 (mtt) cc_final: 0.7953 (mpp) REVERT: A 313 PHE cc_start: 0.8094 (m-80) cc_final: 0.7324 (m-10) REVERT: A 576 MET cc_start: 0.8818 (tpt) cc_final: 0.8561 (tpp) REVERT: A 610 MET cc_start: 0.9135 (mmp) cc_final: 0.8676 (mmp) REVERT: A 781 MET cc_start: 0.9241 (ppp) cc_final: 0.8872 (ppp) REVERT: B 398 MET cc_start: 0.3751 (mmt) cc_final: 0.3258 (mmt) REVERT: B 571 ARG cc_start: 0.8749 (mmm160) cc_final: 0.7618 (mmm160) REVERT: B 719 TYR cc_start: 0.8166 (m-10) cc_final: 0.7807 (m-10) REVERT: B 766 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 835 TYR cc_start: 0.8608 (m-80) cc_final: 0.8316 (m-10) REVERT: B 968 GLN cc_start: 0.5494 (OUTLIER) cc_final: 0.5274 (mt0) REVERT: C 178 GLN cc_start: 0.7472 (tp-100) cc_final: 0.7161 (mp10) REVERT: C 244 ASP cc_start: 0.8021 (m-30) cc_final: 0.7707 (t0) REVERT: C 321 LEU cc_start: 0.8830 (mt) cc_final: 0.8168 (tp) REVERT: C 457 LEU cc_start: 0.9645 (tt) cc_final: 0.9397 (mm) REVERT: C 462 GLU cc_start: 0.9070 (tp30) cc_final: 0.8799 (tp30) REVERT: C 492 MET cc_start: 0.8828 (mtp) cc_final: 0.8627 (mtp) REVERT: C 560 ASN cc_start: 0.7795 (t0) cc_final: 0.7349 (p0) REVERT: C 570 LYS cc_start: 0.9389 (ttmm) cc_final: 0.8899 (tptt) REVERT: C 669 ASP cc_start: 0.7567 (m-30) cc_final: 0.7261 (m-30) REVERT: C 829 PHE cc_start: 0.8626 (t80) cc_final: 0.8376 (t80) REVERT: C 971 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6458 (tt0) REVERT: D 216 LEU cc_start: 0.8937 (tp) cc_final: 0.8667 (tp) REVERT: D 317 MET cc_start: 0.7667 (mmm) cc_final: 0.7183 (tpp) REVERT: D 525 ASP cc_start: 0.7582 (t0) cc_final: 0.7364 (t0) REVERT: D 622 MET cc_start: 0.9184 (ppp) cc_final: 0.8504 (ppp) REVERT: D 899 LYS cc_start: 0.5676 (tptt) cc_final: 0.4792 (mmmt) REVERT: E 120 MET cc_start: 0.7902 (tpp) cc_final: 0.7433 (tpp) REVERT: E 376 ASP cc_start: 0.8604 (m-30) cc_final: 0.8142 (p0) REVERT: E 781 MET cc_start: 0.8897 (ppp) cc_final: 0.8687 (ppp) REVERT: E 850 MET cc_start: 0.6205 (tmm) cc_final: 0.5893 (tmm) REVERT: E 851 ASP cc_start: 0.9128 (p0) cc_final: 0.8451 (t0) REVERT: E 910 ASN cc_start: 0.6779 (OUTLIER) cc_final: 0.6366 (m-40) REVERT: E 951 MET cc_start: 0.7432 (tmm) cc_final: 0.7142 (ttt) REVERT: E 961 MET cc_start: 0.8952 (mtp) cc_final: 0.7712 (tmm) REVERT: F 278 PHE cc_start: 0.7084 (m-80) cc_final: 0.6709 (m-80) REVERT: F 317 MET cc_start: 0.5844 (tpp) cc_final: 0.4088 (mmt) REVERT: F 795 PHE cc_start: 0.7939 (t80) cc_final: 0.7288 (t80) REVERT: F 825 MET cc_start: 0.5077 (tmm) cc_final: 0.4272 (tmm) REVERT: F 1016 TYR cc_start: 0.6760 (m-10) cc_final: 0.5673 (m-80) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.2020 time to fit residues: 117.2917 Evaluate side-chains 241 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 433 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 chunk 544 optimal weight: 0.1980 chunk 12 optimal weight: 20.0000 chunk 536 optimal weight: 30.0000 chunk 193 optimal weight: 0.4980 chunk 453 optimal weight: 0.1980 chunk 262 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 400 optimal weight: 0.8980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 HIS ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN ** 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 482 HIS F 820 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.078278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059982 restraints weight = 253137.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059709 restraints weight = 174084.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059907 restraints weight = 142645.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060259 restraints weight = 125106.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.060413 restraints weight = 112225.614| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43922 Z= 0.117 Angle : 0.655 10.409 59408 Z= 0.331 Chirality : 0.045 0.204 6608 Planarity : 0.004 0.065 7665 Dihedral : 10.031 135.509 6286 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.27 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.11), residues: 5543 helix: 0.26 (0.12), residues: 1767 sheet: -0.77 (0.20), residues: 714 loop : -1.49 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1013 TYR 0.028 0.001 TYR D 347 PHE 0.028 0.001 PHE D 593 TRP 0.016 0.001 TRP B 547 HIS 0.006 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00255 (43921) covalent geometry : angle 0.65493 (59408) hydrogen bonds : bond 0.03457 ( 1512) hydrogen bonds : angle 5.19905 ( 4113) Misc. bond : bond 0.00050 ( 1) ********************** 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 348 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.9134 (mt0) cc_final: 0.8819 (tm-30) REVERT: A 135 MET cc_start: 0.8267 (mmm) cc_final: 0.8009 (mmm) REVERT: A 313 PHE cc_start: 0.8127 (m-80) cc_final: 0.7460 (m-10) REVERT: A 387 LEU cc_start: 0.9066 (tt) cc_final: 0.8701 (mt) REVERT: A 576 MET cc_start: 0.9099 (tpt) cc_final: 0.8834 (tpp) REVERT: A 610 MET cc_start: 0.9174 (mmp) cc_final: 0.8743 (mmp) REVERT: A 632 LEU cc_start: 0.9656 (mt) cc_final: 0.8949 (tp) REVERT: A 637 LEU cc_start: 0.9511 (mt) cc_final: 0.9306 (mt) REVERT: A 781 MET cc_start: 0.9195 (ppp) cc_final: 0.8865 (ppp) REVERT: B 571 ARG cc_start: 0.8693 (mmm160) cc_final: 0.7428 (mmm160) REVERT: B 719 TYR cc_start: 0.8332 (m-10) cc_final: 0.7949 (m-10) REVERT: B 766 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 835 TYR cc_start: 0.8948 (m-80) cc_final: 0.8593 (m-10) REVERT: C 178 GLN cc_start: 0.7539 (tp-100) cc_final: 0.7186 (mm-40) REVERT: C 244 ASP cc_start: 0.8046 (m-30) cc_final: 0.7801 (t0) REVERT: C 321 LEU cc_start: 0.8901 (mt) cc_final: 0.8063 (tt) REVERT: C 438 TYR cc_start: 0.8288 (m-80) cc_final: 0.7897 (m-80) REVERT: C 457 LEU cc_start: 0.9703 (tt) cc_final: 0.9473 (mm) REVERT: C 462 GLU cc_start: 0.9212 (tp30) cc_final: 0.8966 (tp30) REVERT: C 560 ASN cc_start: 0.7790 (t0) cc_final: 0.7267 (p0) REVERT: C 570 LYS cc_start: 0.9461 (ttmm) cc_final: 0.8919 (tptt) REVERT: C 669 ASP cc_start: 0.7902 (m-30) cc_final: 0.7497 (m-30) REVERT: C 824 LYS cc_start: 0.9259 (mmpt) cc_final: 0.9033 (mtpt) REVERT: C 829 PHE cc_start: 0.8897 (t80) cc_final: 0.8660 (t80) REVERT: C 971 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6477 (tt0) REVERT: D 216 LEU cc_start: 0.9130 (tp) cc_final: 0.8825 (tp) REVERT: D 317 MET cc_start: 0.7717 (mmm) cc_final: 0.7470 (tpp) REVERT: D 514 CYS cc_start: 0.9389 (m) cc_final: 0.8609 (p) REVERT: D 525 ASP cc_start: 0.7798 (t0) cc_final: 0.7586 (t0) REVERT: D 554 LEU cc_start: 0.9481 (tt) cc_final: 0.9239 (tp) REVERT: D 622 MET cc_start: 0.9151 (ppp) cc_final: 0.8340 (ppp) REVERT: D 899 LYS cc_start: 0.5731 (tptt) cc_final: 0.4825 (mmmt) REVERT: E 120 MET cc_start: 0.7804 (tpp) cc_final: 0.7453 (tpp) REVERT: E 376 ASP cc_start: 0.8620 (m-30) cc_final: 0.8159 (p0) REVERT: E 850 MET cc_start: 0.6129 (tmm) cc_final: 0.5789 (tmm) REVERT: E 851 ASP cc_start: 0.9222 (p0) cc_final: 0.8578 (t0) REVERT: E 961 MET cc_start: 0.8961 (mtp) cc_final: 0.8007 (ppp) REVERT: F 278 PHE cc_start: 0.7326 (m-80) cc_final: 0.6994 (m-80) REVERT: F 317 MET cc_start: 0.5898 (tpp) cc_final: 0.4312 (mmt) REVERT: F 511 CYS cc_start: 0.9223 (m) cc_final: 0.8893 (p) REVERT: F 612 LEU cc_start: 0.9386 (mt) cc_final: 0.9179 (mt) REVERT: F 795 PHE cc_start: 0.7963 (t80) cc_final: 0.7276 (t80) REVERT: F 825 MET cc_start: 0.5401 (tmm) cc_final: 0.4594 (tmm) REVERT: F 1016 TYR cc_start: 0.6731 (m-10) cc_final: 0.5714 (m-80) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2028 time to fit residues: 122.4473 Evaluate side-chains 251 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 23 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 228 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 542 optimal weight: 50.0000 chunk 541 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 492 optimal weight: 30.0000 chunk 452 optimal weight: 1.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- 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** A 703 GLN C 406 HIS ** C 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 ASN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.077018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059662 restraints weight = 257572.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058723 restraints weight = 197095.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058921 restraints weight = 154246.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059268 restraints weight = 140201.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059363 restraints weight = 126859.786| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43922 Z= 0.171 Angle : 0.689 14.103 59408 Z= 0.352 Chirality : 0.046 0.213 6608 Planarity : 0.005 0.060 7665 Dihedral : 10.188 133.767 6286 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.35 % Favored : 91.63 % Rotamer: Outliers : 0.02 % Allowed : 0.28 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.11), residues: 5543 helix: 0.18 (0.12), residues: 1763 sheet: -0.88 (0.19), residues: 710 loop : -1.55 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1013 TYR 0.027 0.002 TYR A 631 PHE 0.046 0.002 PHE C 770 TRP 0.015 0.002 TRP B 547 HIS 0.005 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00374 (43921) covalent geometry : angle 0.68932 (59408) hydrogen bonds : bond 0.03760 ( 1512) hydrogen bonds : angle 5.39924 ( 4113) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5969.38 seconds wall clock time: 105 minutes 3.87 seconds (6303.87 seconds total)