Starting phenix.real_space_refine on Tue Aug 26 23:27:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0v_16372/08_2025/8c0v_16372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0v_16372/08_2025/8c0v_16372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c0v_16372/08_2025/8c0v_16372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0v_16372/08_2025/8c0v_16372.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0v_16372/08_2025/8c0v_16372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0v_16372/08_2025/8c0v_16372.cif" } resolution = 4.1 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 5 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: 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: "B" 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: "C" 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: {'PCIS': 1, 'PTRANS': 28, '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: "D" 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: "E" 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: "F" 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': 2, 'PTRANS': 49, '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: "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: 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: "E" 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: "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: 8.75, per 1000 atoms: 0.20 Number of scatterers: 43092 At special positions: 0 Unit cell: (190.4, 183.6, 142.8, 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=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 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: 218 helices and 47 sheets defined 41.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 318 through 324 removed outlier: 3.838A pdb=" N ILE A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.527A pdb=" N VAL A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 447 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 483 removed outlier: 4.092A pdb=" N HIS A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 517 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 548 through 566 Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 604 through 620 removed outlier: 4.203A pdb=" N ALA A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 610 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 617 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.714A pdb=" N LEU A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 669 through 675 Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.735A pdb=" N ILE A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 700 " --> pdb=" O TRP A 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 700' Processing helix chain 'A' and resid 702 through 713 removed outlier: 4.087A pdb=" N VAL A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.999A pdb=" N ASN A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 773 through 789 removed outlier: 3.896A pdb=" N GLN A 777 " --> pdb=" O GLY A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 811 through 814 removed outlier: 3.737A pdb=" N THR A 814 " --> pdb=" O THR A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 814' Processing helix chain 'A' and resid 815 through 828 Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 866 through 880 removed outlier: 3.777A pdb=" N LEU A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 905 removed outlier: 3.874A pdb=" N ILE A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 Processing helix chain 'A' and resid 957 through 972 Processing helix chain 'A' and resid 989 through 999 removed outlier: 3.591A pdb=" N GLU A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1022 removed outlier: 4.485A pdb=" N VAL A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS A1011 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.897A pdb=" N VAL B 94 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.600A pdb=" N ILE B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.502A pdb=" N SER B 323 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 340 removed outlier: 4.438A pdb=" N ILE B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.800A pdb=" N ALA B 361 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP B 362 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.132A pdb=" N TYR B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.137A pdb=" N ARG B 455 " --> pdb=" O PHE B 451 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 501 Processing helix chain 'B' and resid 520 through 535 removed outlier: 3.714A pdb=" N TYR B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 564 through 587 removed outlier: 4.157A pdb=" N LEU B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 584 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 585 " --> pdb=" O ASP B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.555A pdb=" N ASN B 601 " --> pdb=" O ASN B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.732A pdb=" N ARG B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 654 through 662 Processing helix chain 'B' and resid 666 through 691 Processing helix chain 'B' and resid 702 through 721 removed outlier: 4.422A pdb=" N LYS B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 749 removed outlier: 3.689A pdb=" N THR B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 789 removed outlier: 3.649A pdb=" N ALA B 782 " --> pdb=" O LYS B 778 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 789 " --> pdb=" O ILE B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 removed outlier: 3.732A pdb=" N ARG B 814 " --> pdb=" O GLU B 810 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 823 " --> pdb=" O LYS B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 848 through 862 removed outlier: 3.786A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 904 through 917 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.880A pdb=" N ALA B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 973 Processing helix chain 'B' and resid 978 through 986 removed outlier: 3.519A pdb=" N ASP B 984 " --> pdb=" O ARG B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 993 Processing helix chain 'B' and resid 998 through 1005 Processing helix chain 'B' and resid 1013 through 1030 removed outlier: 4.159A pdb=" N ALA B1030 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.558A pdb=" N GLU C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.843A pdb=" N THR C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 482 removed outlier: 4.552A pdb=" N LYS C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 517 removed outlier: 3.630A pdb=" N LYS C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS C 511 " --> pdb=" O ILE C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 532 Processing helix chain 'C' and resid 541 through 547 Processing helix chain 'C' and resid 548 through 566 removed outlier: 3.828A pdb=" N LYS C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 591 Processing helix chain 'C' and resid 604 through 619 removed outlier: 3.896A pdb=" N ALA C 609 " --> pdb=" O LYS C 605 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS C 610 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 611 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN C 619 " --> pdb=" O PHE C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 636 removed outlier: 3.877A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU C 636 " --> pdb=" O ASP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 658 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 680 through 685 removed outlier: 3.578A pdb=" N GLY C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 714 removed outlier: 4.583A pdb=" N VAL C 708 " --> pdb=" O ASN C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 719 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 743 through 750 Processing helix chain 'C' and resid 750 through 756 removed outlier: 3.744A pdb=" N GLN C 754 " --> pdb=" O ALA C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 789 Processing helix chain 'C' and resid 813 through 827 Processing helix chain 'C' and resid 842 through 846 removed outlier: 3.855A pdb=" N LEU C 845 " --> pdb=" O ARG C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 869 through 880 removed outlier: 3.614A pdb=" N ILE C 873 " --> pdb=" O GLU C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 905 removed outlier: 4.445A pdb=" N ILE C 901 " --> pdb=" O ASP C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 929 removed outlier: 4.274A pdb=" N GLN C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP C 928 " --> pdb=" O SER C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 934 Processing helix chain 'C' and resid 940 through 944 removed outlier: 4.064A pdb=" N ILE C 944 " --> pdb=" O ASN C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 967 Processing helix chain 'C' and resid 989 through 994 Processing helix chain 'C' and resid 995 through 997 No H-bonds generated for 'chain 'C' and resid 995 through 997' Processing helix chain 'C' and resid 1005 through 1016 removed outlier: 4.062A pdb=" N LEU C1009 " --> pdb=" O SER C1005 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C1015 " --> pdb=" O LYS C1011 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1020 Processing helix chain 'D' and resid 19 through 27 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 119 through 131 removed outlier: 3.818A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.520A pdb=" N SER D 181 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 281 through 287 removed outlier: 4.160A pdb=" N SER D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 339 removed outlier: 3.512A pdb=" N ILE D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 451 through 470 removed outlier: 3.506A pdb=" N ARG D 455 " --> pdb=" O PHE D 451 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 501 Processing helix chain 'D' and resid 521 through 535 Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 562 through 587 removed outlier: 3.548A pdb=" N ILE D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 587 " --> pdb=" O PHE D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 620 through 632 removed outlier: 3.526A pdb=" N LEU D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 638 Processing helix chain 'D' and resid 654 through 662 Processing helix chain 'D' and resid 666 through 689 Processing helix chain 'D' and resid 702 through 721 Processing helix chain 'D' and resid 730 through 734 Processing helix chain 'D' and resid 738 through 748 removed outlier: 3.702A pdb=" N GLY D 742 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.528A pdb=" N LEU D 752 " --> pdb=" O ILE D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 789 Processing helix chain 'D' and resid 799 through 802 Processing helix chain 'D' and resid 807 through 822 Processing helix chain 'D' and resid 832 through 837 removed outlier: 4.168A pdb=" N VAL D 836 " --> pdb=" O GLN D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 847 No H-bonds generated for 'chain 'D' and resid 845 through 847' Processing helix chain 'D' and resid 848 through 863 removed outlier: 4.296A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 904 through 917 Processing helix chain 'D' and resid 926 through 934 removed outlier: 3.615A pdb=" N CYS D 934 " --> pdb=" O LEU D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 967 removed outlier: 3.773A pdb=" N PHE D 943 " --> pdb=" O THR D 939 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 944 " --> pdb=" O GLY D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 993 Processing helix chain 'D' and resid 997 through 1007 Processing helix chain 'D' and resid 1013 through 1026 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 343 through 352 Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 399 through 411 Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'E' and resid 466 through 482 Processing helix chain 'E' and resid 499 through 517 removed outlier: 3.944A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 532 Processing helix chain 'E' and resid 548 through 566 removed outlier: 3.749A pdb=" N ILE E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 591 Processing helix chain 'E' and resid 605 through 617 removed outlier: 3.634A pdb=" N ALA E 609 " --> pdb=" O LYS E 605 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR E 614 " --> pdb=" O LYS E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 658 removed outlier: 4.238A pdb=" N GLU E 646 " --> pdb=" O PRO E 642 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 647 " --> pdb=" O LEU E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 676 removed outlier: 3.678A pdb=" N SER E 676 " --> pdb=" O SER E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 719 removed outlier: 3.978A pdb=" N ASP E 707 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL E 708 " --> pdb=" O ASN E 704 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 709 " --> pdb=" O ALA E 705 " (cutoff:3.500A) Proline residue: E 716 - end of helix Processing helix chain 'E' and resid 719 through 725 removed outlier: 3.579A pdb=" N PHE E 723 " --> pdb=" O TYR E 719 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN E 725 " --> pdb=" O PRO E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 754 Processing helix chain 'E' and resid 765 through 767 No H-bonds generated for 'chain 'E' and resid 765 through 767' Processing helix chain 'E' and resid 771 through 790 removed outlier: 3.954A pdb=" N GLU E 776 " --> pdb=" O ILE E 772 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE E 779 " --> pdb=" O SER E 775 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 780 " --> pdb=" O GLU E 776 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 782 " --> pdb=" O ASN E 778 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER E 788 " --> pdb=" O GLU E 784 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E 790 " --> pdb=" O ALA E 786 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 812 through 825 removed outlier: 3.557A pdb=" N ARG E 816 " --> pdb=" O GLY E 812 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 846 Processing helix chain 'E' and resid 847 through 852 removed outlier: 3.692A pdb=" N LEU E 851 " --> pdb=" O ASP E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 880 Processing helix chain 'E' and resid 898 through 902 removed outlier: 3.562A pdb=" N ALA E 902 " --> pdb=" O LYS E 899 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 933 Processing helix chain 'E' and resid 956 through 968 Processing helix chain 'E' and resid 977 through 986 removed outlier: 3.540A pdb=" N ALA E 980 " --> pdb=" O SER E 977 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA E 981 " --> pdb=" O THR E 978 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU E 983 " --> pdb=" O ALA E 980 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU E 984 " --> pdb=" O ALA E 981 " (cutoff:3.500A) Processing helix chain 'E' and resid 989 through 994 Processing helix chain 'E' and resid 995 through 997 No H-bonds generated for 'chain 'E' and resid 995 through 997' Processing helix chain 'E' and resid 1005 through 1008 Processing helix chain 'E' and resid 1009 through 1015 removed outlier: 4.303A pdb=" N ARG E1013 " --> pdb=" O LEU E1009 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 27 removed outlier: 3.733A pdb=" N GLU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR F 26 " --> pdb=" O ILE F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 91 through 94 Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 118 through 131 removed outlier: 3.773A pdb=" N LYS F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 190 through 194 removed outlier: 4.014A pdb=" N LEU F 194 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 287 removed outlier: 4.323A pdb=" N SER F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 327 through 341 Processing helix chain 'F' and resid 375 through 381 Processing helix chain 'F' and resid 433 through 438 removed outlier: 4.005A pdb=" N TYR F 437 " --> pdb=" O ASN F 433 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR F 438 " --> pdb=" O LEU F 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 433 through 438' Processing helix chain 'F' and resid 451 through 466 removed outlier: 3.689A pdb=" N ARG F 455 " --> pdb=" O PHE F 451 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN F 466 " --> pdb=" O GLU F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 501 Processing helix chain 'F' and resid 509 through 513 Processing helix chain 'F' and resid 522 through 537 removed outlier: 3.545A pdb=" N ILE F 526 " --> pdb=" O THR F 522 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 536 " --> pdb=" O LYS F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 553 Processing helix chain 'F' and resid 565 through 587 Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 603 through 608 removed outlier: 3.546A pdb=" N SER F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 632 removed outlier: 3.756A pdb=" N ARG F 626 " --> pdb=" O ALA F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 640 removed outlier: 4.364A pdb=" N ASP F 640 " --> pdb=" O LEU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 662 removed outlier: 4.238A pdb=" N SER F 662 " --> pdb=" O LEU F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 687 Processing helix chain 'F' and resid 702 through 721 removed outlier: 3.859A pdb=" N VAL F 719 " --> pdb=" O ASN F 715 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER F 720 " --> pdb=" O GLU F 716 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 749 removed outlier: 4.213A pdb=" N GLU F 743 " --> pdb=" O PHE F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 789 Processing helix chain 'F' and resid 808 through 822 Processing helix chain 'F' and resid 844 through 847 Processing helix chain 'F' and resid 848 through 862 removed outlier: 4.609A pdb=" N ASP F 862 " --> pdb=" O LEU F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 870 Processing helix chain 'F' and resid 908 through 918 removed outlier: 4.121A pdb=" N LYS F 918 " --> pdb=" O ALA F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 928 through 933 Processing helix chain 'F' and resid 942 through 973 removed outlier: 4.255A pdb=" N SER F 948 " --> pdb=" O TYR F 944 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 967 " --> pdb=" O GLU F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 986 Processing helix chain 'F' and resid 988 through 993 removed outlier: 3.889A pdb=" N THR F 992 " --> pdb=" O LYS F 989 " (cutoff:3.500A) Processing helix chain 'F' and resid 997 through 1008 removed outlier: 3.503A pdb=" N LEU F1008 " --> pdb=" O ALA F1004 " (cutoff:3.500A) Processing helix chain 'F' and resid 1016 through 1029 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 219 removed outlier: 8.166A pdb=" N ILE A 290 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG A 217 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N HIS A 289 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 236 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 233 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP A 282 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE A 235 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 245 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 310 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE A 215 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 312 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 213 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 314 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.605A pdb=" N ILE A 367 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.605A pdb=" N ILE A 367 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 328 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LYS A 394 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 330 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 396 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 332 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 486 removed outlier: 6.440A pdb=" N PHE A 485 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL A 523 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU A 575 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 522 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER A 577 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 524 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 457 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA A 456 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR A 597 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 458 " --> pdb=" O THR A 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 762 removed outlier: 6.825A pdb=" N GLY A 733 " --> pdb=" O ASP A 857 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N SER A 859 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU A 735 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 861 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR A 737 " --> pdb=" O ILE A 861 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 945 through 946 removed outlier: 4.665A pdb=" N GLU A 945 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N SER B 100 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N CYS B 155 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 102 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 146 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE B 152 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 144 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 8 removed outlier: 8.082A pdb=" N ILE B 66 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER B 4 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL B 68 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR B 6 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 34 " --> pdb=" O CYS B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'B' and resid 202 through 209 removed outlier: 8.422A pdb=" N ILE B 278 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP B 206 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA B 280 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU B 208 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA B 233 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 254 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 295 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 314 through 316 Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AB4, first strand: chain 'B' and resid 503 through 507 removed outlier: 6.710A pdb=" N ALA B 543 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 593 " --> pdb=" O ALA B 543 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE B 545 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER B 595 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 547 " --> pdb=" O SER B 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 647 through 649 Processing sheet with id=AB6, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.673A pdb=" N ASN B 792 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE B 829 " --> pdb=" O ASN B 792 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B 794 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS B 826 " --> pdb=" O PHE B 872 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 874 " --> pdb=" O CYS B 826 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE B 828 " --> pdb=" O ILE B 874 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ALA B 876 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE B 830 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 208 through 219 removed outlier: 7.793A pdb=" N ILE C 290 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG C 217 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 292 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C 219 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N HIS C 289 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER C 236 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS C 245 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 310 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE C 215 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 312 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS C 213 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE C 314 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 360 through 362 removed outlier: 3.830A pdb=" N LEU C 360 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA C 328 " --> pdb=" O GLN C 392 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LYS C 394 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 330 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR C 396 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 332 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 355 through 356 Processing sheet with id=AC1, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.642A pdb=" N VAL C 523 " --> pdb=" O LYS C 487 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LEU C 575 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 522 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER C 577 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 524 " --> pdb=" O SER C 577 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 457 " --> pdb=" O PHE C 576 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY C 578 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 459 " --> pdb=" O GLY C 578 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA C 456 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU C 596 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 458 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 598 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 758 through 762 removed outlier: 6.518A pdb=" N ASN C 758 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE C 795 " --> pdb=" O ASN C 758 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 760 " --> pdb=" O PHE C 795 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS C 792 " --> pdb=" O TYR C 835 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU C 837 " --> pdb=" O CYS C 792 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU C 794 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA C 839 " --> pdb=" O LEU C 794 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE C 796 " --> pdb=" O ALA C 839 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY C 738 " --> pdb=" O THR C 840 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 8 removed outlier: 8.445A pdb=" N ILE D 66 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER D 4 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL D 68 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR D 6 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS D 16 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU D 34 " --> pdb=" O CYS D 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 154 removed outlier: 6.507A pdb=" N THR D 102 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 138 through 140 removed outlier: 3.647A pdb=" N GLY D 161 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 277 through 280 removed outlier: 8.880A pdb=" N ILE D 278 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 206 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA D 280 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU D 208 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 232 through 235 removed outlier: 6.670A pdb=" N ALA D 233 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 351 through 356 removed outlier: 6.355A pdb=" N TRP D 389 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 317 " --> pdb=" O TRP D 389 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N VAL D 312 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N ASN D 420 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE D 314 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR D 422 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG D 316 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 345 through 346 removed outlier: 3.502A pdb=" N LEU D 346 " --> pdb=" O PHE D 407 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE D 407 " --> pdb=" O LEU D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 363 through 365 removed outlier: 3.689A pdb=" N SER E 254 " --> pdb=" O ASN D 364 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 503 through 508 removed outlier: 6.301A pdb=" N HIS D 503 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE D 546 " --> pdb=" O HIS D 503 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 505 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA D 548 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE D 507 " --> pdb=" O ALA D 548 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA D 543 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL D 593 " --> pdb=" O ALA D 543 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE D 545 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N SER D 595 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 547 " --> pdb=" O SER D 595 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 478 " --> pdb=" O GLY D 594 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL D 596 " --> pdb=" O VAL D 478 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 480 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER D 477 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE D 614 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 479 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL D 616 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N HIS D 481 " --> pdb=" O VAL D 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 647 through 649 removed outlier: 7.161A pdb=" N SER D 648 " --> pdb=" O ILE D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 792 through 797 removed outlier: 3.728A pdb=" N ASP D 831 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY D 767 " --> pdb=" O LYS D 895 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU D 897 " --> pdb=" O GLY D 767 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 769 " --> pdb=" O LEU D 897 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 210 through 218 removed outlier: 7.945A pdb=" N ILE E 290 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG E 217 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU E 292 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS E 289 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER E 236 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS E 245 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS E 212 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 367 through 372 removed outlier: 3.560A pdb=" N LYS E 394 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 355 through 357 Processing sheet with id=AD8, first strand: chain 'E' and resid 456 through 460 removed outlier: 5.950A pdb=" N ILE E 457 " --> pdb=" O PHE E 576 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY E 578 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU E 459 " --> pdb=" O GLY E 578 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 485 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL E 523 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'E' and resid 761 through 763 removed outlier: 6.448A pdb=" N VAL E 762 " --> pdb=" O ASP E 797 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'F' and resid 51 through 55 removed outlier: 3.994A pdb=" N LEU F 34 " --> pdb=" O CYS F 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 150 through 151 Processing sheet with id=AE4, first strand: chain 'F' and resid 150 through 151 Processing sheet with id=AE5, first strand: chain 'F' and resid 138 through 140 Processing sheet with id=AE6, first strand: chain 'F' and resid 207 through 209 removed outlier: 6.949A pdb=" N ARG F 260 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 351 through 355 removed outlier: 6.048A pdb=" N VAL F 312 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR F 419 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE F 314 " --> pdb=" O THR F 419 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 344 through 346 removed outlier: 4.704A pdb=" N ARG F 344 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 409 " --> pdb=" O ARG F 344 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 503 through 508 removed outlier: 6.879A pdb=" N VAL F 593 " --> pdb=" O ALA F 543 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE F 545 " --> pdb=" O VAL F 593 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER F 595 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU F 547 " --> pdb=" O SER F 595 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 647 through 648 Processing sheet with id=AF2, first strand: chain 'F' and resid 827 through 830 removed outlier: 3.673A pdb=" N ALA F 876 " --> pdb=" O PHE F 830 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE F 768 " --> pdb=" O GLY F 875 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR F 877 " --> pdb=" O ILE F 768 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE F 770 " --> pdb=" O THR F 877 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU F 769 " --> pdb=" O LEU F 897 " (cutoff:3.500A) 1607 hydrogen bonds defined for protein. 4503 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: 9.37 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13971 1.34 - 1.46: 6724 1.46 - 1.58: 22883 1.58 - 1.70: 55 1.70 - 1.82: 288 Bond restraints: 43921 Sorted by residual: bond pdb=" CB PRO B 41 " pdb=" CG PRO B 41 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.78e+00 bond pdb=" C SER D 541 " pdb=" N PRO D 542 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.14e+00 bond pdb=" CA ASN B 598 " pdb=" CB ASN B 598 " ideal model delta sigma weight residual 1.525 1.553 -0.028 1.77e-02 3.19e+03 2.46e+00 bond pdb=" C LEU E 411 " pdb=" O LEU E 411 " ideal model delta sigma weight residual 1.233 1.240 -0.007 4.80e-03 4.34e+04 2.19e+00 bond pdb=" C ILE C 864 " pdb=" N PRO C 865 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 ... (remaining 43916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 58539 2.59 - 5.18: 764 5.18 - 7.77: 90 7.77 - 10.37: 14 10.37 - 12.96: 1 Bond angle restraints: 59408 Sorted by residual: angle pdb=" CA PRO B 41 " pdb=" N PRO B 41 " pdb=" CD PRO B 41 " ideal model delta sigma weight residual 112.00 104.80 7.20 1.40e+00 5.10e-01 2.65e+01 angle pdb=" CA LYS B 184 " pdb=" CB LYS B 184 " pdb=" CG LYS B 184 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.61e+01 angle pdb=" C TYR C1016 " pdb=" N ASP C1017 " pdb=" CA ASP C1017 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 angle pdb=" O ASN D 200 " pdb=" C ASN D 200 " pdb=" N SER D 201 " ideal model delta sigma weight residual 122.89 118.37 4.52 1.22e+00 6.72e-01 1.38e+01 angle pdb=" CA LEU F1017 " pdb=" CB LEU F1017 " pdb=" CG LEU F1017 " ideal model delta sigma weight residual 116.30 129.26 -12.96 3.50e+00 8.16e-02 1.37e+01 ... (remaining 59403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 25723 33.01 - 66.02: 606 66.02 - 99.03: 77 99.03 - 132.05: 2 132.05 - 165.06: 3 Dihedral angle restraints: 26411 sinusoidal: 10779 harmonic: 15632 Sorted by residual: dihedral pdb=" O2A ADP F1102 " pdb=" O3A ADP F1102 " pdb=" PA ADP F1102 " pdb=" PB ADP F1102 " ideal model delta sinusoidal sigma weight residual 300.00 134.94 165.06 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O2A ADP E1102 " pdb=" O3A ADP E1102 " pdb=" PA ADP E1102 " pdb=" PB ADP E1102 " ideal model delta sinusoidal sigma weight residual -60.00 90.88 -150.88 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP E1102 " pdb=" O3A ADP E1102 " pdb=" PB ADP E1102 " pdb=" PA ADP E1102 " ideal model delta sinusoidal sigma weight residual -60.00 81.36 -141.36 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 26408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5585 0.066 - 0.132: 922 0.132 - 0.198: 93 0.198 - 0.264: 6 0.264 - 0.330: 2 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CB ILE E 621 " pdb=" CA ILE E 621 " pdb=" CG1 ILE E 621 " pdb=" CG2 ILE E 621 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA GLU F1021 " pdb=" N GLU F1021 " pdb=" C GLU F1021 " pdb=" CB GLU F1021 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE F 526 " pdb=" CA ILE F 526 " pdb=" CG1 ILE F 526 " pdb=" CG2 ILE F 526 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 6605 not shown) Planarity restraints: 7665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 200 " -0.037 2.00e-02 2.50e+03 7.18e-02 5.16e+01 pdb=" C ASN D 200 " 0.124 2.00e-02 2.50e+03 pdb=" O ASN D 200 " -0.047 2.00e-02 2.50e+03 pdb=" N SER D 201 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 889 " 0.403 9.50e-02 1.11e+02 1.82e-01 2.49e+01 pdb=" NE ARG B 889 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B 889 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG B 889 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 889 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 523 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C SER D 523 " -0.080 2.00e-02 2.50e+03 pdb=" O SER D 523 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS D 524 " 0.027 2.00e-02 2.50e+03 ... (remaining 7662 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 327 2.54 - 3.13: 36335 3.13 - 3.72: 63906 3.72 - 4.31: 86845 4.31 - 4.90: 140869 Nonbonded interactions: 328282 Sorted by model distance: nonbonded pdb=" O1G ATP B1101 " pdb="MG MG B1103 " model vdw 1.947 2.170 nonbonded pdb=" O1G ATP A1102 " pdb="MG MG A1104 " model vdw 1.954 2.170 nonbonded pdb=" O3G ATP D1101 " pdb="MG MG D1103 " model vdw 1.967 2.170 nonbonded pdb=" O1B ATP B1101 " pdb="MG MG B1103 " model vdw 1.994 2.170 nonbonded pdb=" O1B ATP A1102 " pdb="MG MG A1104 " model vdw 1.995 2.170 ... (remaining 328277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 201 through 1021 or resid 1102 or resid 1104)) selection = (chain 'C' and (resid 201 through 1021 or resid 1102 or resid 1104)) selection = (chain 'E' and (resid 201 through 1101 or resid 1103)) } ncs_group { reference = (chain 'B' and (resid 1 through 1101 or resid 1103)) selection = (chain 'D' and (resid 1 through 1101 or resid 1103)) selection = (chain 'F' and (resid 1 through 1101 or resid 1103)) } 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 35.110 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 43921 Z= 0.140 Angle : 0.754 12.958 59408 Z= 0.404 Chirality : 0.048 0.330 6608 Planarity : 0.007 0.182 7665 Dihedral : 14.633 165.057 16483 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -2.19 (0.11), residues: 5543 helix: -1.28 (0.11), residues: 1814 sheet: -1.28 (0.18), residues: 778 loop : -1.57 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG B 889 TYR 0.037 0.003 TYR E 446 PHE 0.031 0.002 PHE F 391 TRP 0.028 0.002 TRP E 715 HIS 0.007 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00294 (43921) covalent geometry : angle 0.75435 (59408) hydrogen bonds : bond 0.16641 ( 1600) hydrogen bonds : angle 7.09009 ( 4503) *********************** 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 662 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 659 time to evaluate : 1.524 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: A 216 LEU cc_start: 0.8511 (mt) cc_final: 0.8249 (mt) REVERT: A 305 MET cc_start: 0.8587 (tpp) cc_final: 0.8114 (tpp) REVERT: A 514 CYS cc_start: 0.7464 (t) cc_final: 0.7047 (t) REVERT: A 660 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8534 (tpt170) REVERT: A 858 LYS cc_start: 0.7068 (pttm) cc_final: 0.6849 (mtmm) REVERT: A 1001 LYS cc_start: 0.7204 (pttt) cc_final: 0.6496 (tmtt) REVERT: B 17 SER cc_start: 0.8260 (m) cc_final: 0.7929 (p) REVERT: B 76 MET cc_start: 0.6686 (pmm) cc_final: 0.5317 (mmp) REVERT: B 410 ASP cc_start: 0.6275 (t0) cc_final: 0.5665 (m-30) REVERT: B 601 ASN cc_start: 0.8472 (m-40) cc_final: 0.8226 (m-40) REVERT: B 826 CYS cc_start: 0.7246 (p) cc_final: 0.7029 (p) REVERT: B 867 ASP cc_start: 0.7350 (m-30) cc_final: 0.6946 (m-30) REVERT: B 971 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7906 (tm-30) REVERT: C 547 TRP cc_start: 0.5230 (m-10) cc_final: 0.4939 (m-10) REVERT: C 776 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 120 MET cc_start: 0.5739 (pmm) cc_final: 0.5229 (tpp) REVERT: D 143 ASP cc_start: 0.6840 (m-30) cc_final: 0.6524 (t0) REVERT: D 206 ASP cc_start: 0.7646 (t0) cc_final: 0.7336 (t0) REVERT: D 261 LEU cc_start: 0.8103 (tp) cc_final: 0.7526 (mt) REVERT: D 262 VAL cc_start: 0.9426 (p) cc_final: 0.9214 (m) REVERT: D 509 CYS cc_start: 0.7692 (m) cc_final: 0.7086 (m) REVERT: D 669 ASP cc_start: 0.8040 (m-30) cc_final: 0.7650 (m-30) REVERT: D 750 MET cc_start: 0.8805 (mmp) cc_final: 0.8521 (mmm) REVERT: E 279 ILE cc_start: 0.7746 (mt) cc_final: 0.7500 (mt) REVERT: E 347 TYR cc_start: 0.6551 (m-80) cc_final: 0.6211 (m-80) REVERT: E 508 MET cc_start: 0.8068 (tpp) cc_final: 0.7614 (tpp) REVERT: E 579 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8013 (mmtp) REVERT: E 835 TYR cc_start: 0.8580 (m-10) cc_final: 0.8291 (m-80) REVERT: F 339 PHE cc_start: 0.7822 (m-80) cc_final: 0.7312 (m-80) REVERT: F 453 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6879 (p90) outliers start: 3 outliers final: 0 residues processed: 662 average time/residue: 0.2276 time to fit residues: 243.8494 Evaluate side-chains 293 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 0.0970 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A 820 GLN B 310 ASN B 329 ASN B 406 HIS B 449 HIS B 598 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN D 226 ASN D 369 ASN D 573 ASN D 597 ASN D 725 GLN D 788 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS F 169 GLN F 174 ASN F 310 ASN F 384 ASN F 569 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.093175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070637 restraints weight = 175584.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070597 restraints weight = 135320.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070965 restraints weight = 102763.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071232 restraints weight = 96008.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071405 restraints weight = 83833.081| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43921 Z= 0.169 Angle : 0.666 9.030 59408 Z= 0.347 Chirality : 0.046 0.234 6608 Planarity : 0.005 0.057 7665 Dihedral : 10.679 177.537 6286 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.15 % Allowed : 3.43 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.03 (0.11), residues: 5543 helix: 0.21 (0.12), residues: 1844 sheet: -1.09 (0.18), residues: 801 loop : -1.11 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 611 TYR 0.026 0.002 TYR D 128 PHE 0.020 0.002 PHE F 391 TRP 0.018 0.002 TRP F 731 HIS 0.006 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00380 (43921) covalent geometry : angle 0.66610 (59408) hydrogen bonds : bond 0.04358 ( 1600) hydrogen bonds : angle 5.36131 ( 4503) *********************** 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 413 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 406 time to evaluate : 1.939 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 305 MET cc_start: 0.8314 (tpp) cc_final: 0.8052 (tpt) REVERT: A 1001 LYS cc_start: 0.7064 (pttt) cc_final: 0.6461 (tmtt) REVERT: B 17 SER cc_start: 0.8404 (m) cc_final: 0.7985 (p) REVERT: B 20 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8005 (pmt170) REVERT: B 76 MET cc_start: 0.6403 (pmm) cc_final: 0.5083 (mmp) REVERT: B 232 TYR cc_start: 0.7908 (m-80) cc_final: 0.7530 (m-80) REVERT: B 584 THR cc_start: 0.8483 (p) cc_final: 0.8174 (t) REVERT: B 867 ASP cc_start: 0.7562 (m-30) cc_final: 0.7254 (m-30) REVERT: B 971 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7970 (tm-30) REVERT: C 547 TRP cc_start: 0.5364 (m-10) cc_final: 0.5014 (m-10) REVERT: D 1 MET cc_start: 0.5520 (ptm) cc_final: 0.4976 (ptm) REVERT: D 120 MET cc_start: 0.5799 (pmm) cc_final: 0.5360 (tpp) REVERT: D 261 LEU cc_start: 0.8036 (tp) cc_final: 0.7476 (mt) REVERT: D 262 VAL cc_start: 0.9377 (p) cc_final: 0.9129 (m) REVERT: D 669 ASP cc_start: 0.7784 (m-30) cc_final: 0.7381 (m-30) REVERT: E 335 PHE cc_start: 0.6422 (p90) cc_final: 0.6189 (p90) REVERT: E 508 MET cc_start: 0.7754 (tpp) cc_final: 0.7496 (tpp) REVERT: E 548 ASP cc_start: 0.8854 (p0) cc_final: 0.8573 (p0) REVERT: F 360 MET cc_start: 0.7460 (tpp) cc_final: 0.7019 (ttm) REVERT: F 385 ASP cc_start: 0.7187 (p0) cc_final: 0.6967 (p0) REVERT: F 575 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8203 (tm-30) REVERT: F 815 ARG cc_start: 0.8003 (tpt90) cc_final: 0.7305 (tpt90) REVERT: F 955 MET cc_start: 0.7232 (mmp) cc_final: 0.6681 (mtt) outliers start: 7 outliers final: 0 residues processed: 413 average time/residue: 0.2681 time to fit residues: 184.4408 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 : 1.738 ------------------------------------------------------------------------------- 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: 9.9990 chunk 344 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 456 optimal weight: 0.0870 chunk 367 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS B 324 GLN B 406 HIS B 643 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN D 226 ASN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN D 725 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN F 856 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.093243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070164 restraints weight = 173143.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070817 restraints weight = 127335.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071379 restraints weight = 97394.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071858 restraints weight = 82317.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071951 restraints weight = 74454.507| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43921 Z= 0.132 Angle : 0.607 7.588 59408 Z= 0.314 Chirality : 0.045 0.216 6608 Planarity : 0.004 0.054 7665 Dihedral : 10.107 162.439 6286 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.76 (0.11), residues: 5543 helix: 0.53 (0.12), residues: 1870 sheet: -0.95 (0.18), residues: 787 loop : -1.03 (0.12), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 980 TYR 0.024 0.001 TYR F1020 PHE 0.031 0.001 PHE F 390 TRP 0.011 0.001 TRP F 982 HIS 0.006 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00298 (43921) covalent geometry : angle 0.60728 (59408) hydrogen bonds : bond 0.03755 ( 1600) hydrogen bonds : angle 4.97260 ( 4503) *********************** 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 383 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 379 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8331 (tpp) cc_final: 0.8115 (tpt) REVERT: A 1001 LYS cc_start: 0.7038 (pttt) cc_final: 0.6437 (tmtt) REVERT: B 17 SER cc_start: 0.8393 (m) cc_final: 0.7955 (p) REVERT: B 20 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7986 (pmt170) REVERT: B 121 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 232 TYR cc_start: 0.8076 (m-80) cc_final: 0.7626 (m-80) REVERT: B 360 MET cc_start: 0.7339 (mtp) cc_final: 0.7070 (mtt) REVERT: B 551 ASP cc_start: 0.7287 (t0) cc_final: 0.6254 (t0) REVERT: B 567 LYS cc_start: 0.8478 (tptt) cc_final: 0.8052 (tptp) REVERT: B 584 THR cc_start: 0.8440 (p) cc_final: 0.8131 (t) REVERT: B 601 ASN cc_start: 0.8732 (m-40) cc_final: 0.8457 (p0) REVERT: B 750 MET cc_start: 0.7783 (tpp) cc_final: 0.7400 (tpp) REVERT: B 971 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7953 (tm-30) REVERT: C 547 TRP cc_start: 0.5108 (m-10) cc_final: 0.4838 (m-10) REVERT: C 650 GLU cc_start: 0.8075 (tt0) cc_final: 0.7822 (tt0) REVERT: C 690 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7396 (ttmm) REVERT: C 929 LEU cc_start: 0.8629 (mm) cc_final: 0.8338 (mt) REVERT: C 930 SER cc_start: 0.7249 (m) cc_final: 0.6922 (p) REVERT: D 261 LEU cc_start: 0.8005 (tp) cc_final: 0.7397 (mt) REVERT: D 262 VAL cc_start: 0.9395 (p) cc_final: 0.9174 (m) REVERT: D 576 MET cc_start: 0.8360 (tpt) cc_final: 0.8078 (tpp) REVERT: E 335 PHE cc_start: 0.6451 (p90) cc_final: 0.5828 (p90) REVERT: E 508 MET cc_start: 0.7783 (tpp) cc_final: 0.7502 (tpp) REVERT: E 548 ASP cc_start: 0.8811 (p0) cc_final: 0.8521 (p0) REVERT: E 835 TYR cc_start: 0.8510 (m-10) cc_final: 0.8209 (m-80) REVERT: F 385 ASP cc_start: 0.7409 (p0) cc_final: 0.7174 (p0) REVERT: F 815 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7651 (tpt90) REVERT: F 955 MET cc_start: 0.7179 (mmp) cc_final: 0.6718 (mtt) outliers start: 4 outliers final: 0 residues processed: 383 average time/residue: 0.2623 time to fit residues: 169.8246 Evaluate side-chains 246 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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: 20.0000 chunk 463 optimal weight: 40.0000 chunk 247 optimal weight: 9.9990 chunk 497 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 378 optimal weight: 0.9980 chunk 472 optimal weight: 40.0000 chunk 329 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A 972 HIS B 140 HIS B 953 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 725 ASN D 503 HIS D 725 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 788 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 970 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.090864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067586 restraints weight = 175239.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067995 restraints weight = 135400.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068177 restraints weight = 100484.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068527 restraints weight = 95889.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068802 restraints weight = 82764.977| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 43921 Z= 0.215 Angle : 0.675 9.704 59408 Z= 0.349 Chirality : 0.047 0.210 6608 Planarity : 0.005 0.058 7665 Dihedral : 10.036 150.705 6286 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.94 (0.11), residues: 5543 helix: 0.38 (0.12), residues: 1865 sheet: -1.09 (0.18), residues: 782 loop : -1.13 (0.12), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 980 TYR 0.026 0.002 TYR F1020 PHE 0.031 0.002 PHE F 390 TRP 0.016 0.002 TRP F 731 HIS 0.008 0.002 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00492 (43921) covalent geometry : angle 0.67466 (59408) hydrogen bonds : bond 0.04154 ( 1600) hydrogen bonds : angle 5.11296 ( 4503) *********************** 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 328 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8328 (tpp) cc_final: 0.8048 (tpt) REVERT: A 763 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7323 (mtmt) REVERT: A 1001 LYS cc_start: 0.7007 (pttt) cc_final: 0.6514 (tmtt) REVERT: B 971 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8052 (tm-30) REVERT: D 576 MET cc_start: 0.8249 (tpt) cc_final: 0.8018 (tpp) REVERT: D 762 MET cc_start: 0.7370 (ttt) cc_final: 0.7145 (ttt) REVERT: D 951 MET cc_start: 0.7536 (tpp) cc_final: 0.7087 (tpp) REVERT: E 508 MET cc_start: 0.7801 (tpp) cc_final: 0.7513 (tpp) REVERT: E 548 ASP cc_start: 0.8959 (p0) cc_final: 0.8705 (p0) REVERT: E 894 LYS cc_start: 0.5874 (mmtm) cc_final: 0.5637 (pttp) REVERT: F 815 ARG cc_start: 0.7821 (tpt90) cc_final: 0.7586 (tpt90) REVERT: F 955 MET cc_start: 0.7335 (mmp) cc_final: 0.6893 (mtt) outliers start: 2 outliers final: 1 residues processed: 328 average time/residue: 0.2335 time to fit residues: 127.7352 Evaluate side-chains 215 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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: 8.9990 chunk 382 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 507 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 172 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 953 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 725 ASN D 348 GLN D 725 GLN E 327 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 GLN F 598 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.091085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067619 restraints weight = 174797.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068400 restraints weight = 126466.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068416 restraints weight = 97349.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068952 restraints weight = 88414.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069001 restraints weight = 78241.033| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 43921 Z= 0.182 Angle : 0.631 8.552 59408 Z= 0.325 Chirality : 0.045 0.250 6608 Planarity : 0.005 0.056 7665 Dihedral : 9.760 142.541 6286 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.90 (0.11), residues: 5543 helix: 0.49 (0.12), residues: 1852 sheet: -1.17 (0.17), residues: 805 loop : -1.13 (0.12), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E1013 TYR 0.020 0.002 TYR D 528 PHE 0.029 0.002 PHE B 585 TRP 0.011 0.001 TRP A 547 HIS 0.010 0.001 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00413 (43921) covalent geometry : angle 0.63125 (59408) hydrogen bonds : bond 0.03736 ( 1600) hydrogen bonds : angle 4.98480 ( 4503) *********************** 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 329 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7175 (mtmt) REVERT: A 972 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4909 (m90) REVERT: A 1001 LYS cc_start: 0.6927 (pttt) cc_final: 0.6405 (tmtt) REVERT: B 232 TYR cc_start: 0.7797 (m-10) cc_final: 0.7578 (m-80) REVERT: B 584 THR cc_start: 0.8540 (p) cc_final: 0.8272 (t) REVERT: B 750 MET cc_start: 0.7687 (tpp) cc_final: 0.7283 (tpp) REVERT: B 971 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8083 (tm-30) REVERT: D 576 MET cc_start: 0.8591 (tpt) cc_final: 0.8365 (tpp) REVERT: D 750 MET cc_start: 0.8692 (mmp) cc_final: 0.8437 (mmm) REVERT: D 762 MET cc_start: 0.7413 (ttt) cc_final: 0.6973 (ttt) REVERT: D 951 MET cc_start: 0.7492 (tpp) cc_final: 0.7076 (tpp) REVERT: E 508 MET cc_start: 0.7904 (tpp) cc_final: 0.7562 (tpp) REVERT: E 548 ASP cc_start: 0.8936 (p0) cc_final: 0.8685 (p0) REVERT: E 894 LYS cc_start: 0.5935 (mmtm) cc_final: 0.5627 (pttp) REVERT: F 955 MET cc_start: 0.7306 (mmp) cc_final: 0.6883 (mtt) outliers start: 4 outliers final: 0 residues processed: 328 average time/residue: 0.2552 time to fit residues: 141.2492 Evaluate side-chains 216 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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: 1.9990 chunk 372 optimal weight: 9.9990 chunk 330 optimal weight: 0.7980 chunk 402 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 263 optimal weight: 50.0000 chunk 164 optimal weight: 0.0270 chunk 66 optimal weight: 6.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN B 953 ASN C 725 ASN E 295 HIS F 569 GLN F 598 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.092463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070157 restraints weight = 174362.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070321 restraints weight = 130285.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070438 restraints weight = 95852.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070701 restraints weight = 98541.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071057 restraints weight = 83474.547| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43921 Z= 0.117 Angle : 0.596 9.411 59408 Z= 0.303 Chirality : 0.044 0.219 6608 Planarity : 0.004 0.053 7665 Dihedral : 9.270 129.370 6286 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.02 % Allowed : 1.95 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.69 (0.12), residues: 5543 helix: 0.66 (0.12), residues: 1857 sheet: -0.95 (0.18), residues: 782 loop : -1.04 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1013 TYR 0.019 0.001 TYR A 446 PHE 0.027 0.001 PHE F 390 TRP 0.015 0.001 TRP B 731 HIS 0.009 0.001 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00263 (43921) covalent geometry : angle 0.59619 (59408) hydrogen bonds : bond 0.03345 ( 1600) hydrogen bonds : angle 4.75155 ( 4503) *********************** 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 345 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 CYS cc_start: 0.7580 (t) cc_final: 0.7239 (t) REVERT: A 572 ILE cc_start: 0.8963 (mm) cc_final: 0.8750 (mm) REVERT: A 621 ILE cc_start: 0.8589 (mm) cc_final: 0.8273 (tp) REVERT: A 763 LYS cc_start: 0.7426 (ptpt) cc_final: 0.7174 (mtmt) REVERT: A 1001 LYS cc_start: 0.6828 (pttt) cc_final: 0.6393 (tmtt) REVERT: B 232 TYR cc_start: 0.7815 (m-10) cc_final: 0.7370 (m-80) REVERT: B 584 THR cc_start: 0.8499 (p) cc_final: 0.8211 (t) REVERT: B 750 MET cc_start: 0.7746 (tpp) cc_final: 0.7349 (tpp) REVERT: B 815 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.8056 (ptp-110) REVERT: B 971 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8087 (tm-30) REVERT: C 547 TRP cc_start: 0.5102 (m-10) cc_final: 0.4735 (m-10) REVERT: D 88 GLU cc_start: 0.8561 (mp0) cc_final: 0.7694 (mm-30) REVERT: D 505 LEU cc_start: 0.9278 (mt) cc_final: 0.9069 (mp) REVERT: D 576 MET cc_start: 0.8559 (tpt) cc_final: 0.8340 (tpp) REVERT: D 610 MET cc_start: 0.8433 (ppp) cc_final: 0.8169 (ppp) REVERT: D 750 MET cc_start: 0.8597 (mmp) cc_final: 0.8374 (mmm) REVERT: D 762 MET cc_start: 0.7222 (ttt) cc_final: 0.6911 (ttt) REVERT: D 951 MET cc_start: 0.7494 (tpp) cc_final: 0.7083 (tpp) REVERT: E 508 MET cc_start: 0.7715 (tpp) cc_final: 0.7382 (tpp) REVERT: E 548 ASP cc_start: 0.8917 (p0) cc_final: 0.8671 (p0) REVERT: E 869 GLU cc_start: 0.8243 (mp0) cc_final: 0.7938 (mp0) REVERT: E 894 LYS cc_start: 0.5887 (mmtm) cc_final: 0.5554 (pttp) REVERT: F 574 PHE cc_start: 0.8586 (t80) cc_final: 0.8327 (t80) REVERT: F 955 MET cc_start: 0.7270 (mmp) cc_final: 0.6878 (mtt) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.2643 time to fit residues: 153.3211 Evaluate side-chains 229 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 174 optimal weight: 0.2980 chunk 398 optimal weight: 7.9990 chunk 445 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 953 ASN C 725 ASN ** E 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN F 569 GLN F 598 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.092868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070247 restraints weight = 173463.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070499 restraints weight = 123432.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070773 restraints weight = 107691.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071332 restraints weight = 88245.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071418 restraints weight = 76890.170| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43921 Z= 0.112 Angle : 0.587 10.465 59408 Z= 0.297 Chirality : 0.044 0.209 6608 Planarity : 0.004 0.054 7665 Dihedral : 8.922 128.587 6286 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.58 (0.12), residues: 5543 helix: 0.78 (0.12), residues: 1858 sheet: -0.91 (0.18), residues: 786 loop : -0.98 (0.12), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1013 TYR 0.016 0.001 TYR B 232 PHE 0.026 0.001 PHE B 585 TRP 0.018 0.001 TRP C 598 HIS 0.007 0.001 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00249 (43921) covalent geometry : angle 0.58690 (59408) hydrogen bonds : bond 0.03162 ( 1600) hydrogen bonds : angle 4.63430 ( 4503) *********************** 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 333 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 331 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8326 (tpp) cc_final: 0.8047 (tpt) REVERT: A 514 CYS cc_start: 0.7660 (t) cc_final: 0.7280 (t) REVERT: A 572 ILE cc_start: 0.8959 (mm) cc_final: 0.8707 (mm) REVERT: A 621 ILE cc_start: 0.8607 (mm) cc_final: 0.8279 (tp) REVERT: A 763 LYS cc_start: 0.7359 (ptpt) cc_final: 0.7097 (mtmt) REVERT: A 1001 LYS cc_start: 0.6794 (pttt) cc_final: 0.6379 (tmtt) REVERT: B 76 MET cc_start: 0.6170 (pmm) cc_final: 0.4287 (mmm) REVERT: B 232 TYR cc_start: 0.7328 (m-10) cc_final: 0.7085 (m-80) REVERT: B 584 THR cc_start: 0.8512 (p) cc_final: 0.8222 (t) REVERT: B 750 MET cc_start: 0.7747 (tpp) cc_final: 0.7367 (tpp) REVERT: B 961 MET cc_start: 0.8354 (tmm) cc_final: 0.8143 (tmm) REVERT: C 547 TRP cc_start: 0.4921 (m-10) cc_final: 0.4591 (m-10) REVERT: C 846 ILE cc_start: 0.8592 (mt) cc_final: 0.8391 (mt) REVERT: D 88 GLU cc_start: 0.8576 (mp0) cc_final: 0.7727 (mm-30) REVERT: D 505 LEU cc_start: 0.9307 (mt) cc_final: 0.9062 (mp) REVERT: D 555 LEU cc_start: 0.8585 (mm) cc_final: 0.8024 (mt) REVERT: D 576 MET cc_start: 0.8551 (tpt) cc_final: 0.8341 (tpp) REVERT: D 762 MET cc_start: 0.7139 (ttt) cc_final: 0.6883 (ttt) REVERT: D 951 MET cc_start: 0.7778 (tpp) cc_final: 0.7245 (tpp) REVERT: E 398 MET cc_start: 0.6465 (mpp) cc_final: 0.5185 (ptp) REVERT: E 508 MET cc_start: 0.7669 (tpp) cc_final: 0.7330 (tpp) REVERT: E 548 ASP cc_start: 0.8845 (p0) cc_final: 0.8627 (p0) REVERT: E 894 LYS cc_start: 0.5914 (mmtm) cc_final: 0.5562 (pttp) REVERT: F 574 PHE cc_start: 0.8634 (t80) cc_final: 0.8327 (t80) REVERT: F 955 MET cc_start: 0.7309 (mmp) cc_final: 0.6908 (mtp) outliers start: 2 outliers final: 0 residues processed: 332 average time/residue: 0.2598 time to fit residues: 146.2426 Evaluate side-chains 232 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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: 0.0170 chunk 28 optimal weight: 7.9990 chunk 526 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 493 optimal weight: 0.2980 chunk 368 optimal weight: 10.0000 chunk 478 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 436 optimal weight: 5.9990 overall best weight: 2.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 953 ASN C 482 HIS C 483 HIS C 535 GLN C 725 ASN F 598 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.092374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070468 restraints weight = 173425.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070360 restraints weight = 133306.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070325 restraints weight = 110110.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070543 restraints weight = 106467.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071098 restraints weight = 93552.524| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43921 Z= 0.127 Angle : 0.596 9.650 59408 Z= 0.301 Chirality : 0.044 0.190 6608 Planarity : 0.004 0.054 7665 Dihedral : 8.726 125.656 6286 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.48 % Favored : 94.50 % Rotamer: Outliers : 0.02 % Allowed : 0.94 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.56 (0.12), residues: 5543 helix: 0.81 (0.12), residues: 1859 sheet: -0.87 (0.18), residues: 767 loop : -0.99 (0.12), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1013 TYR 0.017 0.001 TYR D 528 PHE 0.023 0.001 PHE B 585 TRP 0.040 0.001 TRP C 598 HIS 0.007 0.001 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00289 (43921) covalent geometry : angle 0.59618 (59408) hydrogen bonds : bond 0.03224 ( 1600) hydrogen bonds : angle 4.63166 ( 4503) *********************** 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 326 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8294 (tpp) cc_final: 0.8034 (tpt) REVERT: A 514 CYS cc_start: 0.7634 (t) cc_final: 0.7216 (t) REVERT: A 572 ILE cc_start: 0.8987 (mm) cc_final: 0.8670 (mm) REVERT: A 763 LYS cc_start: 0.7386 (ptpt) cc_final: 0.7110 (mtmt) REVERT: A 1001 LYS cc_start: 0.6830 (pttt) cc_final: 0.6390 (tmtt) REVERT: B 232 TYR cc_start: 0.7394 (m-10) cc_final: 0.6942 (m-80) REVERT: B 584 THR cc_start: 0.8529 (p) cc_final: 0.8263 (t) REVERT: B 750 MET cc_start: 0.7741 (tpp) cc_final: 0.7350 (tpp) REVERT: B 961 MET cc_start: 0.8332 (tmm) cc_final: 0.8123 (tmm) REVERT: C 547 TRP cc_start: 0.5121 (m-10) cc_final: 0.4760 (m-10) REVERT: C 846 ILE cc_start: 0.8582 (mt) cc_final: 0.8381 (mt) REVERT: D 88 GLU cc_start: 0.8587 (mp0) cc_final: 0.7711 (mm-30) REVERT: D 92 ASP cc_start: 0.7719 (t70) cc_final: 0.7426 (t70) REVERT: D 555 LEU cc_start: 0.8570 (mm) cc_final: 0.8003 (mt) REVERT: D 576 MET cc_start: 0.8561 (tpt) cc_final: 0.8315 (tpp) REVERT: D 750 MET cc_start: 0.8620 (mmp) cc_final: 0.8391 (mmm) REVERT: D 762 MET cc_start: 0.7244 (ttt) cc_final: 0.6955 (ttt) REVERT: E 508 MET cc_start: 0.7649 (tpp) cc_final: 0.7390 (tpp) REVERT: E 548 ASP cc_start: 0.8878 (p0) cc_final: 0.8645 (p0) REVERT: E 869 GLU cc_start: 0.8278 (mp0) cc_final: 0.7985 (mp0) REVERT: E 894 LYS cc_start: 0.5995 (mmtm) cc_final: 0.5649 (pttp) REVERT: F 360 MET cc_start: 0.8139 (ttp) cc_final: 0.7875 (ppp) REVERT: F 574 PHE cc_start: 0.8668 (t80) cc_final: 0.8396 (t80) REVERT: F 955 MET cc_start: 0.7220 (mmp) cc_final: 0.6834 (mtp) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.2527 time to fit residues: 139.1346 Evaluate side-chains 236 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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: 50.0000 chunk 51 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 513 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 529 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 953 ASN C 725 ASN D 151 GLN E 410 HIS E 569 ASN F 384 ASN F 598 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.093550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070970 restraints weight = 172245.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.071560 restraints weight = 133810.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071628 restraints weight = 97095.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072036 restraints weight = 93303.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072148 restraints weight = 83716.374| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 43921 Z= 0.103 Angle : 0.585 10.979 59408 Z= 0.293 Chirality : 0.043 0.231 6608 Planarity : 0.004 0.054 7665 Dihedral : 8.441 124.094 6286 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 0.02 % Allowed : 0.62 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.46 (0.12), residues: 5543 helix: 0.89 (0.12), residues: 1860 sheet: -0.83 (0.18), residues: 769 loop : -0.93 (0.12), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 20 TYR 0.016 0.001 TYR D 528 PHE 0.023 0.001 PHE B 585 TRP 0.034 0.001 TRP C 598 HIS 0.005 0.001 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00226 (43921) covalent geometry : angle 0.58522 (59408) hydrogen bonds : bond 0.02970 ( 1600) hydrogen bonds : angle 4.49033 ( 4503) *********************** 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 343 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8187 (tpp) cc_final: 0.7948 (tpt) REVERT: A 514 CYS cc_start: 0.7736 (t) cc_final: 0.7287 (t) REVERT: A 572 ILE cc_start: 0.8949 (mm) cc_final: 0.8667 (mm) REVERT: A 621 ILE cc_start: 0.8535 (mm) cc_final: 0.8205 (tp) REVERT: A 763 LYS cc_start: 0.7365 (ptpt) cc_final: 0.7129 (mtmt) REVERT: A 1001 LYS cc_start: 0.6740 (pttt) cc_final: 0.6300 (tmtt) REVERT: B 232 TYR cc_start: 0.7379 (m-10) cc_final: 0.7013 (m-80) REVERT: B 584 THR cc_start: 0.8479 (p) cc_final: 0.8189 (t) REVERT: B 750 MET cc_start: 0.7728 (tpp) cc_final: 0.7389 (tpp) REVERT: B 961 MET cc_start: 0.8359 (tmm) cc_final: 0.8135 (tmm) REVERT: C 547 TRP cc_start: 0.4723 (m-10) cc_final: 0.4413 (m-10) REVERT: C 846 ILE cc_start: 0.8555 (mt) cc_final: 0.8342 (mt) REVERT: D 88 GLU cc_start: 0.8502 (mp0) cc_final: 0.7726 (mm-30) REVERT: D 92 ASP cc_start: 0.7788 (t70) cc_final: 0.7468 (t70) REVERT: D 135 MET cc_start: 0.6608 (mpp) cc_final: 0.5912 (mpp) REVERT: D 555 LEU cc_start: 0.8542 (mm) cc_final: 0.7900 (mt) REVERT: D 750 MET cc_start: 0.8583 (mmp) cc_final: 0.8358 (mmm) REVERT: E 508 MET cc_start: 0.7579 (tpp) cc_final: 0.7298 (tpp) REVERT: E 548 ASP cc_start: 0.8802 (p0) cc_final: 0.8570 (p0) REVERT: E 568 ASP cc_start: 0.8541 (p0) cc_final: 0.8312 (p0) REVERT: E 894 LYS cc_start: 0.5932 (mmtm) cc_final: 0.5581 (pttp) REVERT: F 360 MET cc_start: 0.8143 (ttp) cc_final: 0.7905 (ppp) REVERT: F 574 PHE cc_start: 0.8601 (t80) cc_final: 0.8303 (t80) REVERT: F 955 MET cc_start: 0.7188 (mmp) cc_final: 0.6793 (mtp) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.2525 time to fit residues: 147.0735 Evaluate side-chains 239 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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: 2.9990 chunk 386 optimal weight: 10.0000 chunk 544 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 536 optimal weight: 40.0000 chunk 193 optimal weight: 1.9990 chunk 453 optimal weight: 10.0000 chunk 262 optimal weight: 50.0000 chunk 466 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 overall best weight: 6.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN A 482 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN B 406 HIS B 953 ASN C 725 ASN ** D 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN F 169 GLN F 271 ASN F 481 HIS ** F 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 598 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.090211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068279 restraints weight = 174747.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067867 restraints weight = 135521.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068128 restraints weight = 106852.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068416 restraints weight = 103113.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068540 restraints weight = 89511.630| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 43921 Z= 0.239 Angle : 0.694 12.730 59408 Z= 0.355 Chirality : 0.047 0.205 6608 Planarity : 0.005 0.067 7665 Dihedral : 8.953 121.159 6286 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer: Outliers : 0.02 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.85 (0.11), residues: 5543 helix: 0.52 (0.12), residues: 1856 sheet: -1.09 (0.18), residues: 782 loop : -1.10 (0.12), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E1013 TYR 0.038 0.002 TYR D 453 PHE 0.029 0.002 PHE B 585 TRP 0.044 0.002 TRP C 598 HIS 0.008 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00550 (43921) covalent geometry : angle 0.69423 (59408) hydrogen bonds : bond 0.03947 ( 1600) hydrogen bonds : angle 4.99928 ( 4503) ********************** 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 298 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8315 (tpp) cc_final: 0.8090 (tpt) REVERT: A 763 LYS cc_start: 0.7401 (ptpt) cc_final: 0.7114 (mtmt) REVERT: A 1001 LYS cc_start: 0.6954 (pttt) cc_final: 0.6447 (tmtt) REVERT: B 232 TYR cc_start: 0.7921 (m-10) cc_final: 0.7556 (m-80) REVERT: B 584 THR cc_start: 0.8648 (p) cc_final: 0.8376 (t) REVERT: B 750 MET cc_start: 0.7742 (tpp) cc_final: 0.7333 (tpp) REVERT: B 961 MET cc_start: 0.8390 (tmm) cc_final: 0.8183 (tmm) REVERT: B 971 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8127 (tm-30) REVERT: D 92 ASP cc_start: 0.7827 (t70) cc_final: 0.7534 (t70) REVERT: D 555 LEU cc_start: 0.8640 (mm) cc_final: 0.8387 (mp) REVERT: D 750 MET cc_start: 0.8682 (mmp) cc_final: 0.8406 (mmm) REVERT: D 762 MET cc_start: 0.7396 (ttt) cc_final: 0.6985 (ttt) REVERT: E 508 MET cc_start: 0.7817 (tpp) cc_final: 0.7482 (tpp) REVERT: E 548 ASP cc_start: 0.8940 (p0) cc_final: 0.8738 (p0) REVERT: E 894 LYS cc_start: 0.6034 (mmtm) cc_final: 0.5634 (pttp) REVERT: F 574 PHE cc_start: 0.8692 (t80) cc_final: 0.8432 (t80) REVERT: F 955 MET cc_start: 0.7343 (mmp) cc_final: 0.6967 (mtp) outliers start: 1 outliers final: 0 residues processed: 298 average time/residue: 0.2611 time to fit residues: 131.6223 Evaluate side-chains 210 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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: 2.9990 chunk 145 optimal weight: 6.9990 chunk 326 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 542 optimal weight: 0.4980 chunk 541 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 492 optimal weight: 20.0000 chunk 452 optimal weight: 40.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 725 ASN ** D 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 560 GLN F 271 ASN F 481 HIS F 561 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.091170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068636 restraints weight = 175379.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069094 restraints weight = 130884.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069098 restraints weight = 96830.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069345 restraints weight = 95037.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069715 restraints weight = 84406.832| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43921 Z= 0.158 Angle : 0.629 13.012 59408 Z= 0.319 Chirality : 0.045 0.184 6608 Planarity : 0.004 0.054 7665 Dihedral : 8.812 121.385 6286 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.77 % Favored : 94.21 % Rotamer: Outliers : 0.02 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.78 (0.11), residues: 5543 helix: 0.58 (0.12), residues: 1862 sheet: -1.12 (0.18), residues: 782 loop : -1.05 (0.12), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1013 TYR 0.020 0.001 TYR B 232 PHE 0.026 0.001 PHE B 585 TRP 0.035 0.002 TRP C 598 HIS 0.015 0.001 HIS F 481 Details of bonding type rmsd covalent geometry : bond 0.00364 (43921) covalent geometry : angle 0.62902 (59408) hydrogen bonds : bond 0.03512 ( 1600) hydrogen bonds : angle 4.81572 ( 4503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6760.89 seconds wall clock time: 118 minutes 37.04 seconds (7117.04 seconds total)