Starting phenix.real_space_refine on Sat Feb 24 10:05:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0v_16372/02_2024/8c0v_16372_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0v_16372/02_2024/8c0v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0v_16372/02_2024/8c0v_16372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0v_16372/02_2024/8c0v_16372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0v_16372/02_2024/8c0v_16372_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c0v_16372/02_2024/8c0v_16372_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 10 5.21 5 S 195 5.16 5 C 27229 2.51 5 N 7349 2.21 5 O 8275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 829": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "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: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} 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, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "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: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} 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, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 156 Chain: "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: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 4} 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: 21.21, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 18.39 Conformation dependent library (CDL) restraints added in 8.4 seconds 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 215 helices and 46 sheets defined 35.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 438 through 448 removed outlier: 4.011A pdb=" N MET A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR A 446 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 500 through 516 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.763A pdb=" N PHE A 531 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 549 through 565 Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 605 through 619 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) Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 642 through 657 Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 696 through 699 No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 703 through 712 removed outlier: 4.087A pdb=" N VAL A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 744 through 753 Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 799 through 801 No H-bonds generated for 'chain 'A' and resid 799 through 801' Processing helix chain 'A' and resid 812 through 814 No H-bonds generated for 'chain 'A' and resid 812 through 814' Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 867 through 879 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 898 through 905 Processing helix chain 'A' and resid 910 through 931 Processing helix chain 'A' and resid 935 through 938 No H-bonds generated for 'chain 'A' and resid 935 through 938' Processing helix chain 'A' and resid 958 through 971 Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.591A pdb=" N GLU A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1021 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 20 through 25 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 282 through 287 removed outlier: 4.494A pdb=" N SER B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 304 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 359 through 362 removed outlier: 4.504A pdb=" N ASP B 362 " --> pdb=" O SER B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 378 through 381 removed outlier: 4.132A pdb=" N TYR B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 452 through 470 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) removed outlier: 4.212A pdb=" N SER B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 521 through 534 removed outlier: 3.714A pdb=" N TYR B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 565 through 586 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 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 604 through 607 No H-bonds generated for 'chain 'B' and resid 604 through 607' Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.732A pdb=" N ARG B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 703 through 720 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 738 through 748 removed outlier: 3.689A pdb=" N THR B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 788 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) Processing helix chain 'B' and resid 808 through 822 removed outlier: 3.732A pdb=" N ARG B 814 " --> pdb=" O GLU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 885 through 887 No H-bonds generated for 'chain 'B' and resid 885 through 887' Processing helix chain 'B' and resid 905 through 916 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 940 through 972 Processing helix chain 'B' and resid 979 through 985 removed outlier: 3.519A pdb=" N ASP B 984 " --> pdb=" O ARG B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 992 No H-bonds generated for 'chain 'B' and resid 989 through 992' Processing helix chain 'B' and resid 999 through 1006 removed outlier: 4.237A pdb=" N GLU B1006 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1029 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 400 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 447 removed outlier: 3.745A pdb=" N MET C 443 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 447 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 481 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) Processing helix chain 'C' and resid 500 through 516 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 531 removed outlier: 4.203A pdb=" N PHE C 531 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 565 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 587 through 590 No H-bonds generated for 'chain 'C' and resid 587 through 590' Processing helix chain 'C' and resid 605 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 630 through 635 removed outlier: 3.877A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 657 Processing helix chain 'C' and resid 671 through 677 Processing helix chain 'C' and resid 681 through 685 removed outlier: 3.578A pdb=" N GLY C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 681 through 685' Processing helix chain 'C' and resid 701 through 713 removed outlier: 3.841A pdb=" N ASN C 704 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP C 707 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 713 " --> pdb=" O LEU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 718 No H-bonds generated for 'chain 'C' and resid 715 through 718' Processing helix chain 'C' and resid 720 through 723 No H-bonds generated for 'chain 'C' and resid 720 through 723' Processing helix chain 'C' and resid 744 through 749 Processing helix chain 'C' and resid 751 through 755 Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 812 through 826 removed outlier: 3.832A pdb=" N ASP C 815 " --> pdb=" O GLY C 812 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 818 " --> pdb=" O ASP C 815 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 822 " --> pdb=" O ASN C 819 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 826 " --> pdb=" O THR C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 845 No H-bonds generated for 'chain 'C' and resid 843 through 845' Processing helix chain 'C' and resid 848 through 851 No H-bonds generated for 'chain 'C' and resid 848 through 851' Processing helix chain 'C' and resid 870 through 879 Processing helix chain 'C' and resid 898 through 905 Processing helix chain 'C' and resid 911 through 928 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 931 through 933 No H-bonds generated for 'chain 'C' and resid 931 through 933' Processing helix chain 'C' and resid 941 through 943 No H-bonds generated for 'chain 'C' and resid 941 through 943' Processing helix chain 'C' and resid 956 through 966 Processing helix chain 'C' and resid 990 through 996 removed outlier: 4.214A pdb=" N GLU C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA C 996 " --> pdb=" O ASP C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1015 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) Processing helix chain 'C' and resid 1017 through 1019 No H-bonds generated for 'chain 'C' and resid 1017 through 1019' Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.691A pdb=" N HIS D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 282 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 326 through 338 removed outlier: 3.743A pdb=" N ASN D 329 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE D 331 " --> pdb=" O GLN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 368 through 371 No H-bonds generated for 'chain 'D' and resid 368 through 371' Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 452 through 469 removed outlier: 3.515A pdb=" N ILE D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 522 through 537 removed outlier: 4.267A pdb=" N VAL D 536 " --> pdb=" O LYS D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 563 through 586 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) Processing helix chain 'D' and resid 599 through 601 No H-bonds generated for 'chain 'D' and resid 599 through 601' Processing helix chain 'D' and resid 604 through 607 No H-bonds generated for 'chain 'D' and resid 604 through 607' Processing helix chain 'D' and resid 621 through 631 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 634 through 637 No H-bonds generated for 'chain 'D' and resid 634 through 637' Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 667 through 690 removed outlier: 4.252A pdb=" N LYS D 690 " --> pdb=" O TYR D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 720 Processing helix chain 'D' and resid 731 through 733 No H-bonds generated for 'chain 'D' and resid 731 through 733' Processing helix chain 'D' and resid 739 through 747 Processing helix chain 'D' and resid 749 through 752 No H-bonds generated for 'chain 'D' and resid 749 through 752' Processing helix chain 'D' and resid 778 through 788 Processing helix chain 'D' and resid 798 through 801 removed outlier: 3.935A pdb=" N LEU D 801 " --> pdb=" O GLY D 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 798 through 801' Processing helix chain 'D' and resid 808 through 823 removed outlier: 3.629A pdb=" N ALA D 823 " --> pdb=" O LYS D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 836 No H-bonds generated for 'chain 'D' and resid 833 through 836' Processing helix chain 'D' and resid 846 through 862 removed outlier: 4.248A pdb=" N VAL D 849 " --> pdb=" O SER D 846 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET D 850 " --> pdb=" O GLY D 847 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 861 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP D 862 " --> pdb=" O ALA D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 905 through 916 Processing helix chain 'D' and resid 927 through 933 Processing helix chain 'D' and resid 940 through 968 removed outlier: 3.982A pdb=" N TYR D 944 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D 968 " --> pdb=" O LYS D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 992 Processing helix chain 'D' and resid 998 through 1006 Processing helix chain 'D' and resid 1014 through 1025 Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 344 through 351 Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 438 through 447 removed outlier: 4.000A pdb=" N MET E 443 " --> pdb=" O LYS E 440 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 444 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 447 " --> pdb=" O VAL E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 481 Processing helix chain 'E' and resid 500 through 516 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 531 removed outlier: 4.292A pdb=" N PHE E 531 " --> pdb=" O GLU E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 565 removed outlier: 3.749A pdb=" N ILE E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 590 No H-bonds generated for 'chain 'E' and resid 587 through 590' Processing helix chain 'E' and resid 606 through 617 removed outlier: 4.420A pdb=" N TYR E 614 " --> pdb=" O LYS E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 659 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) removed outlier: 3.755A pdb=" N GLU E 659 " --> pdb=" O ASP E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 675 Processing helix chain 'E' and resid 702 through 718 removed outlier: 3.511A pdb=" N LYS E 706 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP E 707 " --> pdb=" O ASN E 704 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP E 715 " --> pdb=" O THR E 712 " (cutoff:3.500A) Proline residue: E 716 - end of helix Processing helix chain 'E' and resid 720 through 725 removed outlier: 4.000A pdb=" N ASN E 725 " --> pdb=" O PRO E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 753 Processing helix chain 'E' and resid 764 through 766 No H-bonds generated for 'chain 'E' and resid 764 through 766' Processing helix chain 'E' and resid 772 through 789 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) Processing helix chain 'E' and resid 799 through 802 No H-bonds generated for 'chain 'E' and resid 799 through 802' Processing helix chain 'E' and resid 813 through 824 Processing helix chain 'E' and resid 843 through 845 No H-bonds generated for 'chain 'E' and resid 843 through 845' Processing helix chain 'E' and resid 848 through 851 No H-bonds generated for 'chain 'E' and resid 848 through 851' Processing helix chain 'E' and resid 867 through 879 Processing helix chain 'E' and resid 899 through 901 No H-bonds generated for 'chain 'E' and resid 899 through 901' Processing helix chain 'E' and resid 913 through 932 Processing helix chain 'E' and resid 957 through 967 Processing helix chain 'E' and resid 978 through 981 removed outlier: 3.977A pdb=" N ALA E 981 " --> pdb=" O THR E 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 978 through 981' Processing helix chain 'E' and resid 983 through 985 No H-bonds generated for 'chain 'E' and resid 983 through 985' Processing helix chain 'E' and resid 990 through 996 removed outlier: 3.671A pdb=" N GLU E 995 " --> pdb=" O ASN E 991 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA E 996 " --> pdb=" O ASP E 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1006 through 1014 removed outlier: 3.628A pdb=" N VAL E1010 " --> pdb=" O SER E1007 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LYS E1011 " --> pdb=" O GLU E1008 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 26 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 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 107 through 114 Processing helix chain 'F' and resid 119 through 130 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 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 282 through 288 removed outlier: 4.323A pdb=" N SER F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE F 288 " --> pdb=" O ILE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 323 No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 325 through 338 removed outlier: 4.737A pdb=" N ASN F 329 " --> pdb=" O CYS F 326 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 332 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 380 removed outlier: 3.949A pdb=" N GLY F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN F 380 " --> pdb=" O ASP F 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 375 through 380' Processing helix chain 'F' and resid 434 through 438 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 434 through 438' Processing helix chain 'F' and resid 452 through 465 removed outlier: 3.705A pdb=" N SER F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 500 Processing helix chain 'F' and resid 509 through 512 No H-bonds generated for 'chain 'F' and resid 509 through 512' Processing helix chain 'F' and resid 523 through 537 removed outlier: 3.584A pdb=" N VAL F 536 " --> pdb=" O LYS F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 566 through 586 Processing helix chain 'F' and resid 599 through 601 No H-bonds generated for 'chain 'F' and resid 599 through 601' Processing helix chain 'F' and resid 604 through 607 No H-bonds generated for 'chain 'F' and resid 604 through 607' Processing helix chain 'F' and resid 621 through 631 removed outlier: 3.756A pdb=" N ARG F 626 " --> pdb=" O ALA F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 639 No H-bonds generated for 'chain 'F' and resid 637 through 639' Processing helix chain 'F' and resid 655 through 661 Processing helix chain 'F' and resid 671 through 686 Processing helix chain 'F' and resid 703 through 720 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 748 removed outlier: 3.551A pdb=" N GLY F 742 " --> pdb=" O PHE F 739 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE F 748 " --> pdb=" O LEU F 745 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 788 Processing helix chain 'F' and resid 809 through 821 Processing helix chain 'F' and resid 845 through 847 No H-bonds generated for 'chain 'F' and resid 845 through 847' Processing helix chain 'F' and resid 849 through 861 Processing helix chain 'F' and resid 909 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 932 Processing helix chain 'F' and resid 941 through 972 removed outlier: 5.068A pdb=" N CYS F 947 " --> pdb=" O TYR F 944 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 949 " --> pdb=" O LEU F 946 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE F 958 " --> pdb=" O MET F 955 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL F 966 " --> pdb=" O GLU F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 979 through 985 Processing helix chain 'F' and resid 989 through 992 removed outlier: 3.889A pdb=" N THR F 992 " --> pdb=" O LYS F 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 989 through 992' Processing helix chain 'F' and resid 998 through 1007 Processing helix chain 'F' and resid 1017 through 1028 Processing sheet with id= A, first strand: chain 'A' and resid 289 through 291 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: 6.524A pdb=" N PHE A 314 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 213 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 312 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE A 215 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 310 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 245 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 371 through 373 Processing sheet with id= C, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= D, 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= E, first strand: chain 'A' and resid 521 through 524 removed outlier: 6.784A pdb=" N ARG A 573 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU A 524 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 575 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE A 458 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR A 597 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 733 through 735 removed outlier: 6.080A pdb=" N ILE A 836 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN A 758 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE A 795 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 760 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 65 through 69 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) removed outlier: 6.061A pdb=" N CYS B 16 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 169 through 174 removed outlier: 6.255A pdb=" N LEU B 104 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE B 152 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 277 through 280 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: 4.644A pdb=" N THR B 295 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 254 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 232 through 235 removed outlier: 6.503A pdb=" N LYS B 263 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR B 235 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE B 265 " --> pdb=" O THR B 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 351 through 356 removed outlier: 7.043A pdb=" N PHE B 313 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.977A pdb=" N LEU B 479 " --> pdb=" O ILE B 614 " (cutoff:3.500A) 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= M, first strand: chain 'B' and resid 647 through 649 removed outlier: 5.658A pdb=" N ILE B 699 " --> pdb=" O SER B 648 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 896 through 898 removed outlier: 8.802A pdb=" N LEU B 897 " --> pdb=" O GLY B 767 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 769 " --> pdb=" O LEU B 897 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 873 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE B 770 " --> pdb=" O VAL B 873 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY B 875 " --> pdb=" O PHE B 770 " (cutoff:3.500A) 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) Processing sheet with id= O, first strand: chain 'C' and resid 289 through 291 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: 7.016A pdb=" N PHE C 314 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS C 213 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 312 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE C 215 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 310 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS C 245 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 391 through 397 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) removed outlier: 3.830A pdb=" N LEU C 360 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 597 through 599 removed outlier: 9.434A pdb=" N TRP C 598 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE C 458 " --> pdb=" O TRP C 598 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 574 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU C 459 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 576 " --> pdb=" O LEU C 459 " (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: 6.581A pdb=" N PHE C 485 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL C 523 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS C 487 " --> pdb=" O VAL C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 858 through 862 removed outlier: 3.810A pdb=" N GLY C 738 " --> pdb=" O THR C 840 " (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: 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) Processing sheet with id= S, first strand: chain 'D' and resid 65 through 69 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: 4.406A pdb=" N LEU D 34 " --> pdb=" O CYS D 55 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS D 16 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 171 through 175 removed outlier: 5.613A pdb=" N LEU D 104 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE D 152 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASN D 106 " --> pdb=" O CYS D 150 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS D 150 " --> pdb=" O ASN D 106 " (cutoff:3.500A) Processing sheet with id= U, 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= V, first strand: chain 'D' and resid 293 through 296 Processing sheet with id= W, first strand: chain 'D' and resid 232 through 235 removed outlier: 6.289A pdb=" N LYS D 263 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR D 235 " --> pdb=" O LYS D 263 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE D 265 " --> pdb=" O THR D 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 311 through 314 removed outlier: 6.654A pdb=" N LYS D 415 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE D 314 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE D 417 " --> pdb=" O ILE D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 351 through 356 Processing sheet with id= Z, first strand: chain 'D' and resid 612 through 616 removed outlier: 3.552A pdb=" N VAL D 616 " --> pdb=" O HIS D 481 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE D 592 " --> pdb=" O VAL D 478 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU D 480 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY D 594 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N SER D 482 " --> pdb=" O GLY D 594 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL D 596 " --> pdb=" O SER D 482 " (cutoff:3.500A) 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) Processing sheet with id= AA, first strand: chain 'D' and resid 647 through 649 removed outlier: 6.064A pdb=" N ILE D 699 " --> pdb=" O SER D 648 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 895 through 897 removed outlier: 8.924A pdb=" N ILE D 768 " --> pdb=" O VAL D 871 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 873 " --> pdb=" O ILE D 768 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE D 770 " --> pdb=" O VAL D 873 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY D 875 " --> pdb=" O PHE D 770 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS D 826 " --> pdb=" O PHE D 872 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE D 874 " --> pdb=" O CYS D 826 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE D 828 " --> pdb=" O ILE D 874 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA D 876 " --> pdb=" O ILE D 828 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE D 830 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN D 792 " --> pdb=" O VAL D 827 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE D 829 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE D 794 " --> pdb=" O PHE D 829 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASP D 831 " --> pdb=" O PHE D 794 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL D 796 " --> pdb=" O ASP D 831 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 290 through 292 removed outlier: 7.775A pdb=" N VAL E 233 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE E 278 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE E 235 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS E 280 " --> pdb=" O ILE E 235 " (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= AD, first strand: chain 'E' and resid 367 through 373 removed outlier: 3.560A pdb=" N LYS E 394 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 355 through 357 Processing sheet with id= AF, first strand: chain 'E' and resid 456 through 460 removed outlier: 6.739A pdb=" N VAL E 574 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU E 459 " --> pdb=" O VAL E 574 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE E 576 " --> pdb=" O LEU E 459 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 734 through 736 Processing sheet with id= AH, first strand: chain 'E' and resid 761 through 763 removed outlier: 6.398A pdb=" N PHE E 795 " --> pdb=" O VAL E 762 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AJ, 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= AK, first strand: chain 'F' and resid 169 through 173 Processing sheet with id= AL, first strand: chain 'F' and resid 138 through 140 Processing sheet with id= AM, first strand: chain 'F' and resid 207 through 209 removed outlier: 5.991A pdb=" N ILE F 278 " --> pdb=" O GLU F 208 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS F 263 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR F 235 " --> pdb=" O LYS F 263 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE F 265 " --> pdb=" O THR F 235 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 312 through 315 Processing sheet with id= AO, 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= AP, first strand: chain 'F' and resid 351 through 355 Processing sheet with id= AQ, first strand: chain 'F' and resid 478 through 481 Processing sheet with id= AR, first strand: chain 'F' and resid 503 through 508 Processing sheet with id= AS, first strand: chain 'F' and resid 768 through 771 removed outlier: 3.673A pdb=" N ALA F 876 " --> pdb=" O PHE F 830 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'F' and resid 251 through 254 removed outlier: 6.949A pdb=" N ARG F 260 " --> pdb=" O VAL F 253 " (cutoff:3.500A) 1259 hydrogen bonds defined for protein. 3366 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: 16.55 Time building geometry restraints manager: 19.75 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: 97.50 - 105.97: 1011 105.97 - 114.44: 25688 114.44 - 122.91: 28820 122.91 - 131.38: 3809 131.38 - 139.85: 80 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: 335 2.54 - 3.13: 36595 3.13 - 3.72: 64163 3.72 - 4.31: 87554 4.31 - 4.90: 140999 Nonbonded interactions: 329646 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 329641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 1021 or resid 1101 or resid 1103)) } ncs_group { reference = (chain 'B' and (resid 1 through 1030 or resid 1101 or resid 1103)) selection = (chain 'D' and (resid 1 through 1030 or resid 1101 or resid 1103)) selection = (chain 'F' and (resid 1 through 1030 or resid 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: 3.630 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: 14.800 Check model and map are aligned: 0.640 Set scattering table: 0.350 Process input model: 113.710 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.870 ------------------------------------------------------------------------------- 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= 0.193 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 : 6.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (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 TRP 0.028 0.002 TRP E 715 HIS 0.007 0.001 HIS F 140 PHE 0.031 0.002 PHE F 391 TYR 0.037 0.003 TYR E 446 ARG 0.038 0.002 ARG B 889 *********************** 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 fitting. rotamer outliers: 3 poor density : 659 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.7048 (t) REVERT: A 660 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8536 (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: 0.7928 (p) REVERT: B 76 MET cc_start: 0.6686 (pmm) cc_final: 0.5314 (mmp) REVERT: B 410 ASP cc_start: 0.6275 (t0) cc_final: 0.5662 (m-30) REVERT: B 601 ASN cc_start: 0.8472 (m-40) cc_final: 0.8224 (m-40) REVERT: B 826 CYS cc_start: 0.7246 (p) cc_final: 0.7038 (p) REVERT: B 867 ASP cc_start: 0.7350 (m-30) cc_final: 0.6936 (m-30) REVERT: B 971 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7905 (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: 0.5230 (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: 0.7337 (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: 0.7088 (m) REVERT: D 669 ASP cc_start: 0.8040 (m-30) cc_final: 0.7650 (m-30) REVERT: E 279 ILE cc_start: 0.7746 (mt) cc_final: 0.7507 (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: 0.7616 (tpp) REVERT: E 579 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8012 (mmtp) REVERT: E 835 TYR cc_start: 0.8580 (m-10) cc_final: 0.8290 (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: 0.6880 (p90) outliers start: 3 outliers final: 0 residues processed: 662 average time/residue: 0.5745 time to fit residues: 610.2518 Evaluate side-chains 293 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 5.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 468 optimal weight: 30.0000 chunk 420 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 143 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 435 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 264 optimal weight: 20.0000 chunk 323 optimal weight: 1.9990 chunk 504 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 366 GLN ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN B 329 ASN B 406 HIS B 598 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN D 226 ASN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN F 364 ASN F 384 ASN F 561 GLN F 569 GLN ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.062 43921 Z= 0.249 Angle : 0.641 8.107 59408 Z= 0.330 Chirality : 0.046 0.227 6608 Planarity : 0.004 0.056 7665 Dihedral : 10.476 177.660 6286 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.15 % Allowed : 3.66 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.11), residues: 5543 helix: 0.04 (0.12), residues: 1807 sheet: -1.01 (0.18), residues: 776 loop : -1.12 (0.12), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 731 HIS 0.005 0.001 HIS B 127 PHE 0.021 0.002 PHE F 391 TYR 0.026 0.002 TYR D 128 ARG 0.007 0.001 ARG D 611 *********************** 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 405 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 398 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8543 (tpp) cc_final: 0.8336 (tpt) REVERT: A 714 GLU cc_start: 0.6342 (tm-30) cc_final: 0.6042 (tm-30) REVERT: A 1001 LYS cc_start: 0.7061 (pttt) cc_final: 0.6447 (tmtt) REVERT: B 17 SER cc_start: 0.8262 (m) cc_final: 0.7856 (p) REVERT: B 20 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8019 (ptp90) REVERT: B 76 MET cc_start: 0.6876 (pmm) cc_final: 0.5343 (mmp) REVERT: B 121 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 232 TYR cc_start: 0.8056 (m-80) cc_final: 0.7552 (m-80) REVERT: B 360 MET cc_start: 0.7799 (mtp) cc_final: 0.7470 (mtt) REVERT: B 410 ASP cc_start: 0.6115 (t0) cc_final: 0.5588 (m-30) REVERT: B 576 MET cc_start: 0.8585 (tpp) cc_final: 0.8346 (tpt) REVERT: B 601 ASN cc_start: 0.8728 (m-40) cc_final: 0.8398 (m-40) REVERT: B 971 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7969 (tm-30) REVERT: C 547 TRP cc_start: 0.5372 (m-10) cc_final: 0.4997 (m-10) REVERT: D 5 LEU cc_start: 0.8067 (tp) cc_final: 0.7856 (tp) REVERT: D 120 MET cc_start: 0.5746 (pmm) cc_final: 0.5324 (tpp) REVERT: D 143 ASP cc_start: 0.7298 (m-30) cc_final: 0.6613 (t0) REVERT: D 261 LEU cc_start: 0.8116 (tp) cc_final: 0.7535 (mt) REVERT: D 262 VAL cc_start: 0.9469 (p) cc_final: 0.9261 (m) REVERT: D 750 MET cc_start: 0.8589 (mmm) cc_final: 0.8286 (mmm) REVERT: E 508 MET cc_start: 0.8035 (tpp) cc_final: 0.7631 (tpp) REVERT: E 852 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7564 (mtp85) REVERT: F 339 PHE cc_start: 0.8101 (m-80) cc_final: 0.7820 (m-80) REVERT: F 360 MET cc_start: 0.7474 (tpp) cc_final: 0.7068 (ttm) REVERT: F 385 ASP cc_start: 0.7168 (p0) cc_final: 0.6918 (p0) REVERT: F 575 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8242 (tm-30) REVERT: F 815 ARG cc_start: 0.8016 (tpt90) cc_final: 0.7322 (tpt90) REVERT: F 955 MET cc_start: 0.7198 (mmp) cc_final: 0.6684 (mtt) outliers start: 7 outliers final: 0 residues processed: 405 average time/residue: 0.5420 time to fit residues: 365.4482 Evaluate side-chains 252 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 4.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 280 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 419 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 504 optimal weight: 5.9990 chunk 545 optimal weight: 8.9990 chunk 449 optimal weight: 10.0000 chunk 500 optimal weight: 10.0000 chunk 172 optimal weight: 0.0470 chunk 405 optimal weight: 5.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- 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 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 953 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 573 ASN D 725 GLN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 43921 Z= 0.278 Angle : 0.624 8.837 59408 Z= 0.320 Chirality : 0.045 0.217 6608 Planarity : 0.004 0.054 7665 Dihedral : 10.127 154.629 6286 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 5543 helix: 0.18 (0.12), residues: 1834 sheet: -0.91 (0.18), residues: 753 loop : -1.09 (0.12), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 731 HIS 0.008 0.001 HIS F 635 PHE 0.024 0.002 PHE F 390 TYR 0.030 0.002 TYR D 128 ARG 0.008 0.001 ARG E1013 *********************** 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 342 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 5.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 ARG cc_start: 0.8846 (tpt170) cc_final: 0.8599 (tpt170) REVERT: A 1001 LYS cc_start: 0.6991 (pttt) cc_final: 0.6431 (tmtt) REVERT: B 76 MET cc_start: 0.6834 (pmm) cc_final: 0.5320 (mmp) REVERT: B 121 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 232 TYR cc_start: 0.7986 (m-80) cc_final: 0.7458 (m-80) REVERT: B 410 ASP cc_start: 0.6063 (t0) cc_final: 0.5515 (m-30) REVERT: B 508 ASP cc_start: 0.8525 (p0) cc_final: 0.8261 (p0) REVERT: B 576 MET cc_start: 0.8632 (tpp) cc_final: 0.8425 (tpt) REVERT: B 601 ASN cc_start: 0.8812 (m-40) cc_final: 0.8496 (m-40) REVERT: B 750 MET cc_start: 0.7735 (tpp) cc_final: 0.7341 (tpp) REVERT: D 261 LEU cc_start: 0.8130 (tp) cc_final: 0.7893 (tp) REVERT: D 339 PHE cc_start: 0.7372 (t80) cc_final: 0.7014 (t80) REVERT: D 409 ILE cc_start: 0.7218 (pt) cc_final: 0.6979 (pt) REVERT: D 576 MET cc_start: 0.8714 (tpt) cc_final: 0.8400 (tpp) REVERT: D 750 MET cc_start: 0.8522 (mmm) cc_final: 0.8229 (mmm) REVERT: D 980 ARG cc_start: 0.5708 (tpt90) cc_final: 0.5406 (tpm170) REVERT: E 335 PHE cc_start: 0.6703 (p90) cc_final: 0.6103 (p90) REVERT: E 508 MET cc_start: 0.8024 (tpp) cc_final: 0.7603 (tpp) REVERT: E 548 ASP cc_start: 0.8996 (p0) cc_final: 0.8700 (p0) REVERT: E 894 LYS cc_start: 0.5740 (mmtm) cc_final: 0.5428 (pttp) REVERT: F 815 ARG cc_start: 0.7942 (tpt90) cc_final: 0.7270 (tpt90) REVERT: F 955 MET cc_start: 0.7205 (mmp) cc_final: 0.6792 (mtt) outliers start: 2 outliers final: 0 residues processed: 342 average time/residue: 0.5598 time to fit residues: 318.9936 Evaluate side-chains 240 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 5.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 498 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 262 optimal weight: 50.0000 chunk 55 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 339 optimal weight: 7.9990 chunk 506 optimal weight: 8.9990 chunk 536 optimal weight: 50.0000 chunk 264 optimal weight: 20.0000 chunk 480 optimal weight: 4.9990 chunk 144 optimal weight: 0.0470 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS B 406 HIS ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN D 226 ASN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN E 284 GLN E 758 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 43921 Z= 0.270 Angle : 0.619 8.383 59408 Z= 0.318 Chirality : 0.045 0.209 6608 Planarity : 0.005 0.056 7665 Dihedral : 9.794 147.417 6286 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 5543 helix: 0.30 (0.12), residues: 1798 sheet: -1.04 (0.18), residues: 792 loop : -1.09 (0.12), residues: 2953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 731 HIS 0.008 0.001 HIS D 754 PHE 0.020 0.002 PHE E 723 TYR 0.027 0.002 TYR F 382 ARG 0.009 0.001 ARG F 530 *********************** 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 334 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 5.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8498 (tpp) cc_final: 0.8277 (tpt) REVERT: A 772 ILE cc_start: 0.6940 (mp) cc_final: 0.6739 (mt) REVERT: A 1001 LYS cc_start: 0.6895 (pttt) cc_final: 0.6422 (tmtt) REVERT: B 410 ASP cc_start: 0.5994 (t0) cc_final: 0.5484 (m-30) REVERT: B 508 ASP cc_start: 0.8544 (p0) cc_final: 0.8295 (p0) REVERT: B 576 MET cc_start: 0.8574 (tpp) cc_final: 0.8364 (tpt) REVERT: B 601 ASN cc_start: 0.8876 (m-40) cc_final: 0.8564 (m-40) REVERT: B 744 ILE cc_start: 0.8833 (mt) cc_final: 0.8471 (mt) REVERT: B 750 MET cc_start: 0.7691 (tpp) cc_final: 0.7273 (tpp) REVERT: B 961 MET cc_start: 0.8517 (tmm) cc_final: 0.8295 (tmm) REVERT: B 971 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8085 (tm-30) REVERT: C 690 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7657 (ttmm) REVERT: C 929 LEU cc_start: 0.8889 (mm) cc_final: 0.8555 (mt) REVERT: D 261 LEU cc_start: 0.7988 (tp) cc_final: 0.7767 (tp) REVERT: D 339 PHE cc_start: 0.7492 (t80) cc_final: 0.7150 (t80) REVERT: D 576 MET cc_start: 0.8719 (tpt) cc_final: 0.8462 (tpp) REVERT: D 750 MET cc_start: 0.8604 (mmm) cc_final: 0.8318 (mmm) REVERT: D 762 MET cc_start: 0.7624 (ttt) cc_final: 0.7365 (ttt) REVERT: D 850 MET cc_start: 0.6570 (ptt) cc_final: 0.6178 (mtt) REVERT: D 980 ARG cc_start: 0.5796 (tpt90) cc_final: 0.5286 (tpm170) REVERT: E 223 MET cc_start: 0.8166 (mpp) cc_final: 0.7932 (mpp) REVERT: E 508 MET cc_start: 0.8101 (tpp) cc_final: 0.7657 (tpp) REVERT: E 548 ASP cc_start: 0.9045 (p0) cc_final: 0.8672 (p0) REVERT: E 894 LYS cc_start: 0.5809 (mmtm) cc_final: 0.5571 (pttp) REVERT: F 207 LEU cc_start: 0.7585 (tp) cc_final: 0.7380 (tp) REVERT: F 339 PHE cc_start: 0.8198 (m-80) cc_final: 0.7856 (m-10) REVERT: F 955 MET cc_start: 0.7306 (mmp) cc_final: 0.6960 (mtt) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.5518 time to fit residues: 306.7193 Evaluate side-chains 225 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 5.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 446 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 399 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 457 optimal weight: 4.9990 chunk 370 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 273 optimal weight: 30.0000 chunk 481 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN C 725 ASN D 348 GLN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 HIS E 327 ASN E 410 HIS E 863 ASN ** F 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 43921 Z= 0.369 Angle : 0.687 9.579 59408 Z= 0.352 Chirality : 0.047 0.245 6608 Planarity : 0.005 0.066 7665 Dihedral : 9.897 143.864 6286 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.11), residues: 5543 helix: 0.07 (0.12), residues: 1780 sheet: -1.13 (0.18), residues: 799 loop : -1.25 (0.12), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 731 HIS 0.009 0.001 HIS D 754 PHE 0.028 0.002 PHE F 628 TYR 0.023 0.002 TYR F1020 ARG 0.007 0.001 ARG B 815 *********************** 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 326 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8495 (tpp) cc_final: 0.8241 (tpt) REVERT: A 401 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8474 (tp30) REVERT: A 452 ILE cc_start: 0.9366 (pt) cc_final: 0.9155 (pt) REVERT: A 1001 LYS cc_start: 0.6890 (pttt) cc_final: 0.6447 (tmtt) REVERT: B 76 MET cc_start: 0.6734 (pmm) cc_final: 0.5144 (mmp) REVERT: B 232 TYR cc_start: 0.8024 (m-10) cc_final: 0.7691 (m-80) REVERT: B 410 ASP cc_start: 0.5889 (t0) cc_final: 0.5336 (m-30) REVERT: B 508 ASP cc_start: 0.8631 (p0) cc_final: 0.8310 (p0) REVERT: B 601 ASN cc_start: 0.8858 (m-40) cc_final: 0.8512 (m-40) REVERT: B 750 MET cc_start: 0.7547 (tpp) cc_final: 0.7104 (tpp) REVERT: B 971 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8114 (tm-30) REVERT: C 690 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7743 (ttmm) REVERT: C 929 LEU cc_start: 0.8940 (mm) cc_final: 0.8605 (mt) REVERT: D 261 LEU cc_start: 0.7942 (tp) cc_final: 0.7719 (tp) REVERT: D 576 MET cc_start: 0.8719 (tpt) cc_final: 0.8474 (tpp) REVERT: D 750 MET cc_start: 0.8731 (mmm) cc_final: 0.8420 (mmm) REVERT: D 819 LYS cc_start: 0.8777 (tptt) cc_final: 0.8249 (tppt) REVERT: D 850 MET cc_start: 0.6802 (ptt) cc_final: 0.6441 (mtt) REVERT: E 508 MET cc_start: 0.8045 (tpp) cc_final: 0.7636 (tpp) REVERT: E 548 ASP cc_start: 0.9115 (p0) cc_final: 0.8784 (p0) REVERT: E 894 LYS cc_start: 0.5852 (mmtm) cc_final: 0.5536 (pttp) REVERT: F 207 LEU cc_start: 0.7643 (tp) cc_final: 0.7430 (tp) REVERT: F 598 ASN cc_start: 0.8634 (t0) cc_final: 0.8296 (m-40) REVERT: F 955 MET cc_start: 0.7364 (mmp) cc_final: 0.7094 (mtt) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.5305 time to fit residues: 292.7199 Evaluate side-chains 222 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 180 optimal weight: 0.0870 chunk 483 optimal weight: 0.9980 chunk 106 optimal weight: 0.0670 chunk 314 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 536 optimal weight: 50.0000 chunk 445 optimal weight: 40.0000 chunk 248 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 281 optimal weight: 40.0000 overall best weight: 2.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 HIS ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 561 GLN F 569 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43921 Z= 0.197 Angle : 0.590 8.662 59408 Z= 0.300 Chirality : 0.044 0.219 6608 Planarity : 0.004 0.050 7665 Dihedral : 9.265 143.856 6286 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5543 helix: 0.35 (0.12), residues: 1784 sheet: -0.99 (0.18), residues: 782 loop : -1.13 (0.12), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 547 HIS 0.006 0.001 HIS E 483 PHE 0.025 0.001 PHE B 165 TYR 0.019 0.001 TYR D 528 ARG 0.010 0.000 ARG E1013 *********************** 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 338 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 5.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8428 (tpp) cc_final: 0.8192 (tpt) REVERT: A 572 ILE cc_start: 0.9035 (mm) cc_final: 0.8823 (mt) REVERT: A 763 LYS cc_start: 0.7599 (ptpt) cc_final: 0.7212 (mtmt) REVERT: A 1001 LYS cc_start: 0.6714 (pttt) cc_final: 0.6383 (tmtt) REVERT: B 76 MET cc_start: 0.6817 (pmm) cc_final: 0.5330 (mmp) REVERT: B 232 TYR cc_start: 0.7756 (m-10) cc_final: 0.7290 (m-80) REVERT: B 335 LEU cc_start: 0.9267 (tp) cc_final: 0.9021 (pp) REVERT: B 410 ASP cc_start: 0.5973 (t0) cc_final: 0.5433 (m-30) REVERT: B 457 LEU cc_start: 0.8646 (tt) cc_final: 0.8316 (mp) REVERT: B 508 ASP cc_start: 0.8640 (p0) cc_final: 0.8373 (p0) REVERT: B 567 LYS cc_start: 0.8587 (tptt) cc_final: 0.8114 (tptp) REVERT: B 601 ASN cc_start: 0.8792 (m-40) cc_final: 0.8483 (m-40) REVERT: B 750 MET cc_start: 0.7690 (tpp) cc_final: 0.7263 (tpp) REVERT: B 961 MET cc_start: 0.8501 (tmm) cc_final: 0.8268 (tmm) REVERT: B 971 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8110 (tm-30) REVERT: C 690 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7611 (ttmm) REVERT: C 929 LEU cc_start: 0.8969 (mm) cc_final: 0.8614 (mt) REVERT: D 92 ASP cc_start: 0.7773 (t70) cc_final: 0.7438 (t70) REVERT: D 261 LEU cc_start: 0.7846 (tp) cc_final: 0.7597 (tp) REVERT: D 576 MET cc_start: 0.8690 (tpt) cc_final: 0.8444 (tpp) REVERT: D 610 MET cc_start: 0.8693 (ppp) cc_final: 0.8367 (ppp) REVERT: D 750 MET cc_start: 0.8719 (mmm) cc_final: 0.8464 (mmm) REVERT: D 762 MET cc_start: 0.7742 (ttm) cc_final: 0.7360 (ttt) REVERT: D 819 LYS cc_start: 0.8873 (tppt) cc_final: 0.8634 (tptt) REVERT: D 850 MET cc_start: 0.6786 (ptt) cc_final: 0.6499 (mtt) REVERT: D 980 ARG cc_start: 0.6227 (tpt90) cc_final: 0.5591 (tpm170) REVERT: E 398 MET cc_start: 0.6340 (mpp) cc_final: 0.5110 (ptp) REVERT: E 508 MET cc_start: 0.7943 (tpp) cc_final: 0.7494 (tpp) REVERT: E 548 ASP cc_start: 0.9067 (p0) cc_final: 0.8660 (p0) REVERT: E 869 GLU cc_start: 0.8251 (mp0) cc_final: 0.7823 (mp0) REVERT: E 894 LYS cc_start: 0.5938 (mmtm) cc_final: 0.5590 (pttp) REVERT: F 207 LEU cc_start: 0.7592 (tp) cc_final: 0.7357 (tp) REVERT: F 574 PHE cc_start: 0.8591 (t80) cc_final: 0.8334 (t80) REVERT: F 598 ASN cc_start: 0.8593 (t0) cc_final: 0.8262 (m-40) REVERT: F 955 MET cc_start: 0.7386 (mmp) cc_final: 0.7146 (mtt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.5253 time to fit residues: 298.8584 Evaluate side-chains 230 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 5.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 517 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 392 optimal weight: 50.0000 chunk 303 optimal weight: 20.0000 chunk 452 optimal weight: 40.0000 chunk 299 optimal weight: 5.9990 chunk 534 optimal weight: 2.9990 chunk 334 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN C 968 GLN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 ASN E 327 ASN F 178 GLN F 349 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43921 Z= 0.225 Angle : 0.598 16.780 59408 Z= 0.303 Chirality : 0.044 0.234 6608 Planarity : 0.004 0.050 7665 Dihedral : 9.092 141.665 6286 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.04 % Allowed : 1.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5543 helix: 0.42 (0.12), residues: 1784 sheet: -0.96 (0.18), residues: 785 loop : -1.13 (0.12), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 928 HIS 0.005 0.001 HIS D 754 PHE 0.019 0.001 PHE E 513 TYR 0.033 0.001 TYR D 128 ARG 0.011 0.000 ARG E1013 *********************** 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 322 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 320 time to evaluate : 5.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8428 (tpp) cc_final: 0.8201 (tpt) REVERT: A 572 ILE cc_start: 0.9083 (mm) cc_final: 0.8873 (mt) REVERT: A 763 LYS cc_start: 0.7603 (ptpt) cc_final: 0.7184 (mtmt) REVERT: A 772 ILE cc_start: 0.6974 (mp) cc_final: 0.6759 (mt) REVERT: A 1001 LYS cc_start: 0.6731 (pttt) cc_final: 0.6398 (tmtt) REVERT: B 76 MET cc_start: 0.6832 (pmm) cc_final: 0.5304 (mmp) REVERT: B 232 TYR cc_start: 0.7872 (m-10) cc_final: 0.7573 (m-80) REVERT: B 335 LEU cc_start: 0.9277 (tp) cc_final: 0.9021 (pp) REVERT: B 601 ASN cc_start: 0.8758 (m-40) cc_final: 0.8413 (m-40) REVERT: B 750 MET cc_start: 0.7677 (tpp) cc_final: 0.7231 (tpp) REVERT: B 961 MET cc_start: 0.8502 (tmm) cc_final: 0.8285 (tmm) REVERT: B 971 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8126 (tm-30) REVERT: C 690 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7505 (ttmm) REVERT: C 929 LEU cc_start: 0.8983 (mm) cc_final: 0.8641 (mt) REVERT: D 92 ASP cc_start: 0.7795 (t70) cc_final: 0.7417 (t70) REVERT: D 261 LEU cc_start: 0.7809 (tp) cc_final: 0.7529 (tp) REVERT: D 576 MET cc_start: 0.8760 (tpt) cc_final: 0.8527 (tpp) REVERT: D 610 MET cc_start: 0.8735 (ppp) cc_final: 0.8460 (ppp) REVERT: D 750 MET cc_start: 0.8717 (mmm) cc_final: 0.8469 (mmm) REVERT: D 762 MET cc_start: 0.7722 (ttm) cc_final: 0.7439 (ttt) REVERT: D 850 MET cc_start: 0.6768 (ptt) cc_final: 0.6419 (mtt) REVERT: E 398 MET cc_start: 0.6397 (mpp) cc_final: 0.5125 (ptp) REVERT: E 508 MET cc_start: 0.7905 (tpp) cc_final: 0.7482 (tpp) REVERT: E 548 ASP cc_start: 0.9074 (p0) cc_final: 0.8685 (p0) REVERT: E 869 GLU cc_start: 0.8230 (mp0) cc_final: 0.7815 (mp0) REVERT: E 894 LYS cc_start: 0.5973 (mmtm) cc_final: 0.5646 (pttp) REVERT: F 256 MET cc_start: 0.4090 (mmm) cc_final: 0.3456 (mmm) REVERT: F 574 PHE cc_start: 0.8584 (t80) cc_final: 0.8318 (t80) REVERT: F 598 ASN cc_start: 0.8657 (t0) cc_final: 0.8270 (m-40) REVERT: F 955 MET cc_start: 0.7395 (mmp) cc_final: 0.7146 (mtt) outliers start: 2 outliers final: 1 residues processed: 322 average time/residue: 0.5281 time to fit residues: 285.4206 Evaluate side-chains 229 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 330 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 319 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 364 optimal weight: 0.0270 chunk 264 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 420 optimal weight: 5.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN C 968 GLN ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43921 Z= 0.201 Angle : 0.587 8.688 59408 Z= 0.297 Chirality : 0.044 0.209 6608 Planarity : 0.004 0.051 7665 Dihedral : 8.843 139.682 6286 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.02 % Allowed : 0.92 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 5543 helix: 0.47 (0.12), residues: 1784 sheet: -0.87 (0.18), residues: 787 loop : -1.12 (0.12), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 928 HIS 0.005 0.001 HIS D 754 PHE 0.025 0.001 PHE F 339 TYR 0.019 0.001 TYR F1020 ARG 0.009 0.000 ARG E1013 *********************** 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 322 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 5.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8400 (tpp) cc_final: 0.8187 (tpt) REVERT: A 572 ILE cc_start: 0.9090 (mm) cc_final: 0.8862 (mt) REVERT: A 585 ASN cc_start: 0.8658 (t0) cc_final: 0.8412 (t0) REVERT: A 763 LYS cc_start: 0.7515 (ptpt) cc_final: 0.7122 (mtmt) REVERT: A 1001 LYS cc_start: 0.6683 (pttt) cc_final: 0.6362 (tmtt) REVERT: B 76 MET cc_start: 0.6736 (pmm) cc_final: 0.5174 (mmp) REVERT: B 335 LEU cc_start: 0.9266 (tp) cc_final: 0.9015 (pp) REVERT: B 567 LYS cc_start: 0.8630 (tptt) cc_final: 0.8161 (tptp) REVERT: B 601 ASN cc_start: 0.8681 (m-40) cc_final: 0.8305 (m-40) REVERT: B 750 MET cc_start: 0.7711 (tpp) cc_final: 0.7263 (tpp) REVERT: B 961 MET cc_start: 0.8512 (tmm) cc_final: 0.8277 (tmm) REVERT: B 971 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8134 (tm-30) REVERT: C 443 MET cc_start: 0.8966 (mpp) cc_final: 0.8445 (mpp) REVERT: C 690 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7442 (ttmm) REVERT: C 929 LEU cc_start: 0.9001 (mm) cc_final: 0.8628 (mt) REVERT: D 92 ASP cc_start: 0.7828 (t70) cc_final: 0.7432 (t70) REVERT: D 261 LEU cc_start: 0.7802 (tp) cc_final: 0.7509 (tp) REVERT: D 576 MET cc_start: 0.8765 (tpt) cc_final: 0.8526 (tpp) REVERT: D 610 MET cc_start: 0.8742 (ppp) cc_final: 0.8510 (ppp) REVERT: D 750 MET cc_start: 0.8724 (mmm) cc_final: 0.8495 (mmm) REVERT: D 762 MET cc_start: 0.7692 (ttm) cc_final: 0.7431 (ttt) REVERT: D 850 MET cc_start: 0.6820 (ptt) cc_final: 0.6469 (mtt) REVERT: E 398 MET cc_start: 0.6462 (mpp) cc_final: 0.5180 (ptp) REVERT: E 508 MET cc_start: 0.7902 (tpp) cc_final: 0.7470 (tpp) REVERT: E 548 ASP cc_start: 0.9055 (p0) cc_final: 0.8661 (p0) REVERT: E 869 GLU cc_start: 0.8211 (mp0) cc_final: 0.7814 (mp0) REVERT: E 894 LYS cc_start: 0.5941 (mmtm) cc_final: 0.5586 (pttp) REVERT: F 509 CYS cc_start: 0.7467 (m) cc_final: 0.7202 (m) REVERT: F 574 PHE cc_start: 0.8566 (t80) cc_final: 0.8298 (t80) REVERT: F 598 ASN cc_start: 0.8645 (t0) cc_final: 0.8280 (m-40) REVERT: F 955 MET cc_start: 0.7416 (mmp) cc_final: 0.7190 (mtt) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.5430 time to fit residues: 296.6248 Evaluate side-chains 223 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 486 optimal weight: 6.9990 chunk 512 optimal weight: 9.9990 chunk 467 optimal weight: 1.9990 chunk 498 optimal weight: 20.0000 chunk 300 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 391 optimal weight: 0.0270 chunk 152 optimal weight: 6.9990 chunk 450 optimal weight: 20.0000 chunk 471 optimal weight: 9.9990 chunk 496 optimal weight: 9.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN C 968 GLN F 271 ASN ** F 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43921 Z= 0.188 Angle : 0.575 8.510 59408 Z= 0.291 Chirality : 0.043 0.198 6608 Planarity : 0.004 0.050 7665 Dihedral : 8.616 137.688 6286 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 0.02 % Allowed : 0.77 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 5543 helix: 0.56 (0.13), residues: 1769 sheet: -0.83 (0.18), residues: 774 loop : -1.07 (0.12), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 928 HIS 0.005 0.001 HIS B 127 PHE 0.017 0.001 PHE F 338 TYR 0.024 0.001 TYR D 128 ARG 0.010 0.000 ARG B 815 *********************** 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 327 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8377 (tpp) cc_final: 0.8171 (tpt) REVERT: A 572 ILE cc_start: 0.9065 (mm) cc_final: 0.8815 (mt) REVERT: A 585 ASN cc_start: 0.8679 (t0) cc_final: 0.8449 (t0) REVERT: A 763 LYS cc_start: 0.7454 (ptpt) cc_final: 0.7092 (mtmt) REVERT: A 1001 LYS cc_start: 0.6668 (pttt) cc_final: 0.6357 (tmtt) REVERT: B 1 MET cc_start: 0.7150 (ppp) cc_final: 0.6912 (ppp) REVERT: B 76 MET cc_start: 0.6781 (pmm) cc_final: 0.5264 (mmp) REVERT: B 232 TYR cc_start: 0.7637 (m-10) cc_final: 0.7414 (m-80) REVERT: B 567 LYS cc_start: 0.8648 (tptt) cc_final: 0.8188 (tptp) REVERT: B 601 ASN cc_start: 0.8635 (m-40) cc_final: 0.8268 (m-40) REVERT: B 750 MET cc_start: 0.7764 (tpp) cc_final: 0.7307 (tpp) REVERT: B 815 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.8019 (ptp-110) REVERT: B 961 MET cc_start: 0.8512 (tmm) cc_final: 0.8272 (tmm) REVERT: B 971 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8121 (tm-30) REVERT: C 443 MET cc_start: 0.8936 (mpp) cc_final: 0.8466 (mpp) REVERT: C 929 LEU cc_start: 0.8993 (mm) cc_final: 0.8632 (mt) REVERT: D 92 ASP cc_start: 0.7883 (t70) cc_final: 0.7523 (t70) REVERT: D 576 MET cc_start: 0.8759 (tpt) cc_final: 0.8506 (tpp) REVERT: D 610 MET cc_start: 0.8773 (ppp) cc_final: 0.8561 (ppp) REVERT: D 750 MET cc_start: 0.8718 (mmm) cc_final: 0.8492 (mmm) REVERT: D 762 MET cc_start: 0.7671 (ttm) cc_final: 0.7375 (ttt) REVERT: D 850 MET cc_start: 0.6926 (ptt) cc_final: 0.6582 (mtt) REVERT: E 398 MET cc_start: 0.6487 (mpp) cc_final: 0.5152 (ptp) REVERT: E 508 MET cc_start: 0.7851 (tpp) cc_final: 0.7439 (tpp) REVERT: E 548 ASP cc_start: 0.9045 (p0) cc_final: 0.8677 (p0) REVERT: E 869 GLU cc_start: 0.8204 (mp0) cc_final: 0.7816 (mp0) REVERT: E 894 LYS cc_start: 0.5950 (mmtm) cc_final: 0.5597 (pttp) REVERT: F 509 CYS cc_start: 0.7436 (m) cc_final: 0.7202 (m) REVERT: F 574 PHE cc_start: 0.8535 (t80) cc_final: 0.8264 (t80) REVERT: F 598 ASN cc_start: 0.8633 (t0) cc_final: 0.8312 (m-40) REVERT: F 955 MET cc_start: 0.7421 (mmp) cc_final: 0.7161 (mtt) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.5215 time to fit residues: 286.8100 Evaluate side-chains 222 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 327 optimal weight: 6.9990 chunk 527 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 552 optimal weight: 40.0000 chunk 508 optimal weight: 0.8980 chunk 440 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 340 optimal weight: 0.0170 chunk 269 optimal weight: 0.0060 overall best weight: 1.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN A 754 GLN ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 968 GLN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN F 271 ASN ** F 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43921 Z= 0.158 Angle : 0.572 10.255 59408 Z= 0.287 Chirality : 0.043 0.238 6608 Planarity : 0.004 0.053 7665 Dihedral : 8.342 136.304 6286 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 5543 helix: 0.65 (0.13), residues: 1786 sheet: -0.72 (0.18), residues: 769 loop : -1.02 (0.12), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 928 HIS 0.005 0.001 HIS F 754 PHE 0.014 0.001 PHE D 339 TYR 0.018 0.001 TYR F1020 ARG 0.012 0.000 ARG D 276 ********************** 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 329 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 5.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ILE cc_start: 0.8997 (mm) cc_final: 0.8737 (mt) REVERT: A 585 ASN cc_start: 0.8651 (t0) cc_final: 0.8430 (t0) REVERT: A 621 ILE cc_start: 0.8588 (mm) cc_final: 0.8281 (tp) REVERT: A 763 LYS cc_start: 0.7307 (ptpt) cc_final: 0.6951 (mtmt) REVERT: A 1001 LYS cc_start: 0.6623 (pttt) cc_final: 0.6340 (tmtt) REVERT: B 76 MET cc_start: 0.6742 (pmm) cc_final: 0.5274 (mmp) REVERT: B 232 TYR cc_start: 0.7650 (m-10) cc_final: 0.7380 (m-80) REVERT: B 567 LYS cc_start: 0.8676 (tptt) cc_final: 0.8215 (tptp) REVERT: B 601 ASN cc_start: 0.8564 (m-40) cc_final: 0.8236 (m-40) REVERT: B 750 MET cc_start: 0.7782 (tpp) cc_final: 0.7368 (tpp) REVERT: B 961 MET cc_start: 0.8517 (tmm) cc_final: 0.8272 (tmm) REVERT: B 971 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8108 (tm-30) REVERT: C 317 MET cc_start: 0.3674 (ppp) cc_final: 0.3205 (ppp) REVERT: C 443 MET cc_start: 0.8912 (mpp) cc_final: 0.8505 (mpp) REVERT: C 929 LEU cc_start: 0.8986 (mm) cc_final: 0.8603 (mt) REVERT: D 92 ASP cc_start: 0.7870 (t70) cc_final: 0.7502 (t70) REVERT: D 576 MET cc_start: 0.8729 (tpt) cc_final: 0.8476 (tpp) REVERT: D 610 MET cc_start: 0.8764 (ppp) cc_final: 0.8518 (ppp) REVERT: D 762 MET cc_start: 0.7595 (ttm) cc_final: 0.7350 (ttt) REVERT: D 850 MET cc_start: 0.6953 (ptt) cc_final: 0.6609 (mtt) REVERT: E 380 LEU cc_start: 0.7586 (tp) cc_final: 0.6851 (pt) REVERT: E 398 MET cc_start: 0.6449 (mpp) cc_final: 0.5289 (ptp) REVERT: E 508 MET cc_start: 0.7817 (tpp) cc_final: 0.7407 (tpp) REVERT: E 548 ASP cc_start: 0.9026 (p0) cc_final: 0.8680 (p0) REVERT: E 869 GLU cc_start: 0.8216 (mp0) cc_final: 0.7832 (mp0) REVERT: E 894 LYS cc_start: 0.5992 (mmtm) cc_final: 0.5654 (pttp) REVERT: F 509 CYS cc_start: 0.7410 (m) cc_final: 0.7168 (m) REVERT: F 574 PHE cc_start: 0.8535 (t80) cc_final: 0.8228 (t80) REVERT: F 598 ASN cc_start: 0.8590 (t0) cc_final: 0.8263 (m-40) REVERT: F 955 MET cc_start: 0.7460 (mmp) cc_final: 0.7174 (mtt) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.5353 time to fit residues: 296.6473 Evaluate side-chains 227 residues out of total 4958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 349 optimal weight: 9.9990 chunk 469 optimal weight: 10.0000 chunk 134 optimal weight: 0.3980 chunk 405 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 440 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 452 optimal weight: 40.0000 chunk 55 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN C 968 GLN ** D 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** F 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.091370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068698 restraints weight = 174524.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069215 restraints weight = 128832.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069538 restraints weight = 93266.044| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43921 Z= 0.225 Angle : 0.590 10.388 59408 Z= 0.298 Chirality : 0.044 0.232 6608 Planarity : 0.004 0.053 7665 Dihedral : 8.387 133.692 6286 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 5543 helix: 0.60 (0.13), residues: 1780 sheet: -0.83 (0.18), residues: 792 loop : -1.07 (0.12), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 547 HIS 0.005 0.001 HIS D 754 PHE 0.024 0.001 PHE C 723 TYR 0.021 0.001 TYR F1020 ARG 0.009 0.000 ARG E1013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7811.13 seconds wall clock time: 144 minutes 46.03 seconds (8686.03 seconds total)